Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold7111.1
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: 8186
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Found at i:307 original size:44 final size:44
Alignment explanation
Indices: 259--678 Score: 363
Period size: 44 Copynumber: 9.6 Consensus size: 44
249 TCTTCGATCC
* *
259 GTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTCAACTT
1 GTTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACTT
* * * * *
303 GTTCCCTATAAGCACAGGGATGTC--ATGCTGAAATCTTCGATCTA
1 GTTCCCTATAAGCACAGGGATGCCAAAT-CTGATATTTTC-AACTT
* * * * * * * * * *
347 CTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCGA-TCC
1 GTTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACT-T
*
391 GTTCCCTATAAGCACAGGGATGCCAAATCT-ATTGTTTTCAACTT
1 GTTCCCTATAAGCACAGGGATGCCAAATCTGA-TATTTTCAACTT
*
435 GTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACTT
1 GTTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACTT
* * *
479 GTTCCCTATAAGCACAGGGATGCC--ATGCTGAAATCTTTGATC-T
1 GTTCCCTATAAGCACAGGGATGCCAAAT-CTGATAT-TTTCAACTT
* * * * * * * * *
522 GCTTCACTATAAGCCCAGGAATGTCAGATCTGCTATCTTCGA-TCC
1 G-TTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACT-T
* *
567 GTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACTC
1 GTTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACTT
* * * * *
611 GTTCCCTATAAGCACAGGGATACC-ATTCTAAAATCTTCAACTT
1 GTTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACTT
654 GTTCCCTATAAGCACAGGGATGCCA
1 GTTCCCTATAAGCACAGGGATGCCA
679 TGCTGAAATC
Statistics
Matches: 300, Mismatches: 59, Indels: 34
0.76 0.15 0.09
Matches are distributed among these distances:
42 4 0.01
43 51 0.17
44 223 0.74
45 18 0.06
46 4 0.01
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (44 bp):
GTTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACTT
Found at i:465 original size:176 final size:176
Alignment explanation
Indices: 258--737 Score: 811
Period size: 176 Copynumber: 2.7 Consensus size: 176
248 ATCTTCGATC
*
258 CGTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGA
1 CGTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACTTGTTCCCTATAAGCACAGGGA
* *
323 TGTCATGCTGAAATCTTCGATCTACTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCGA
66 TGCCATGCTGAAATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCGA
388 TCCGTTCCCTATAAGCACAGGGATGCCAAATCT-ATTGTTTTCAACT
131 TCCGTTCCCTATAAGCACAGGGATGCCAAATCTGA-TGTTTTCAACT
*
434 TGTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACTTGTTCCCTATAAGCACAGGGA
1 CGTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACTTGTTCCCTATAAGCACAGGGA
* * *
499 TGCCATGCTGAAATCTTTGATCTGCTTCACTATAAGCCCAGGAATGTCAGATCTGCTATCTTCGA
66 TGCCATGCTGAAATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCGA
564 TCCGTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACT
131 TCCGTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACT
* * * ** *
610 CGTTCCCTATAAGCACAGGGATACC-ATTCTAAAATCTTCAACTTGTTCCCTATAAGCACAGGGA
1 CGTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACTTGTTCCCTATAAGCACAGGGA
*
674 TGCCATGCTGAAATCTTGGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCG
66 TGCCATGCTGAAATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCG
738 GTCTGCTCCT
Statistics
Matches: 286, Mismatches: 17, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
175 95 0.33
176 190 0.66
177 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (176 bp):
CGTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACTTGTTCCCTATAAGCACAGGGA
TGCCATGCTGAAATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCGA
TCCGTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACT
Found at i:491 original size:132 final size:132
Alignment explanation
Indices: 223--628 Score: 480
Period size: 132 Copynumber: 3.1 Consensus size: 132
213 TGCTTCACTG
*
223 TAAGCACAGGAATGTCAGATTTGCTATCTTCGATCCGTTCCCTATAAGCACAGGGATGCCAAATC
1 TAAGCACAGGAATGTCAGATCTGCTATCTTCGATCCGTTCCCTATAAGCACAGGGATGCCAAATC
* ** * * *
288 TGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGTC--ATGCTGAAATCTTCGATCTACTTC
66 TGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCAAAT-CTGATGTTTTC-AACTAGTTC
* *
351 ACTG
129 CCTA
355 TAAGCACAGGAATGTCAGATCTGCTATCTTCGATCCGTTCCCTATAAGCACAGGGATGCCAAATC
1 TAAGCACAGGAATGTCAGATCTGCTATCTTCGATCCGTTCCCTATAAGCACAGGGATGCCAAATC
** *
420 TATTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACTTGTTCCC
66 TGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACTAGTTCCC
485 TA
131 TA
* * ** * * * * * * *
487 TAAGCACAGGGATG-C-CATGCTGAAATCTTTGATCTGCTTCACTATAAGCCCAGGAATGTCAGA
1 TAAGCACAGGAATGTCAGAT-CTGCTATCTTCGATCCG-TTCCCTATAAGCACAGGGATGCCAAA
* * * * *
550 TCTGCTATCTTCGA-TCCGTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACTCGTT
64 TCTGCTGTTTTCAACT-TGTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACTAGTT
614 CCCTA
128 CCCTA
619 TAAGCACAGG
1 TAAGCACAGG
629 GATACCATTC
Statistics
Matches: 239, Mismatches: 30, Indels: 10
0.86 0.11 0.04
Matches are distributed among these distances:
130 2 0.01
131 15 0.06
132 212 0.89
133 8 0.03
134 2 0.01
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (132 bp):
TAAGCACAGGAATGTCAGATCTGCTATCTTCGATCCGTTCCCTATAAGCACAGGGATGCCAAATC
TGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACTAGTTCCC
TA
Found at i:875 original size:68 final size:68
Alignment explanation
Indices: 790--988 Score: 294
Period size: 68 Copynumber: 2.9 Consensus size: 68
780 TCTTCTTCCA
* * * *
790 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCTCTCCAATGCCATTTCTGGAAGAAGAGGT
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAATGCCATTTCAGGAAGAAAAGAT
*
855 -TT
66 CCT
* * *
857 GTTGAAACTTCAAGGAGATCTGTTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGAAGAAAAGA
1 -CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAATGCCATTTCAGGAAGAAAAGA
922 TCCT
65 TCCT
*
926 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAATGCCATTTCAGGGA-AAAAGA
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAATGCCATTTCAGGAAGAAAAGA
989 AATTTGTAAT
Statistics
Matches: 118, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
67 6 0.05
68 111 0.94
69 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.28
Consensus pattern (68 bp):
CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAATGCCATTTCAGGAAGAAAAGAT
CCT
Found at i:1118 original size:43 final size:43
Alignment explanation
Indices: 1044--1994 Score: 479
Period size: 43 Copynumber: 21.8 Consensus size: 43
1034 GCCCATCATC
* * * *
1044 TTCGATCTATTTCCCAACTGCTTAAGGGGTTAAGATCTGTAAA
1 TTCGATCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAA
* * * *
1087 TTCAACCTGTTACCCTACTGGTTAGGGGGTTAAGATTTGTAAA
1 TTCGATCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAA
* * * *
1130 TCTTC-AGCCTGTTACCCTACTGCTTAGGGGTTTAAGGTTTGTAAA
1 --TTCGA-TCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAA
* ** * **
1175 TTCG-GCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCAT-CATT
1 TTCGATC-TGTTACCCTACTGCTTAGGGGGTT-AAGATC-TGTAAA
** *
1219 TTTTATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAA
1 TTCGATCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAA
** * * * * *
1262 TCTTTAGTCAGTTACCCTACTTCTTAAGGGTTTAAG-GCTTGTAAA
1 T-TCGA-TCTGTTACCCTACTGCTTAGGGGGTTAAGATC-TGTAAA
* * * ** * **
1307 TTTG-GCTTGTTACCCTACTGCTTAGTGGGTTAAAGCCCAT-CATC
1 TTCGATC-TGTTACCCTACTGCTTAGGGGGTT-AAGATC-TGTAAA
* * *
1351 TTTGATCTGTTTCCCTACTGCTTAAGGGGTTAAGATCTGTAAA
1 TTCGATCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAA
* * * *
1394 TCTTC-AGCCTGTTACCCTACTACTTAGGGCGTTAAG-GCTTGTAAA
1 --TTCGA-TCTGTTACCCTACTGCTTAGGGGGTTAAGATC-TGTAAA
* * * ** * **
1439 TTTG-GCTTGTTACCCTACTACTTAGGGGGTTAAAGCCCAT-CATC
1 TTCGATC-TGTTACCCTACTGCTTAGGGGGTT-AAGATC-TGTAAA
* * ** **
1483 TTTGATCTATTTTCCTACTGCTTAGGGGGTTAAGATCT-TCATC
1 TTCGATCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGT-AAA
* * * *
1526 TTCGATCTGTTTCCCTACTGCTTAGGGAGATAAGATCTG-CAA
1 TTCGATCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAA
*** * * **
1568 TTC-AGTCTGTTACCCTACCAATTAGGGGTTTAAGACCCT-TCATC
1 TTCGA-TCTGTTACCCTACTGCTTAGGGGGTTAAGA-TCTGT-AAA
* *
1612 TTTGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAA
1 TTCGATCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAA
* *
1655 TCTTC-AGCCTGTTACCCTACTGCTTAGGGGGTTAAG-GCTTGTAAA
1 --TTCGA-TCTGTTACCCTACTGCTTAGGGGGTTAAGATC-TGTAAA
* * ** * **
1700 TT-TAGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCAT-CATC
1 TTCGATC-TGTTACCCTACTGCTTAGGGGGTT-AAGATC-TGTAAA
* * **
1744 TTCAATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCT-TCATC
1 TTCGATCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGT-AAA
* **
1787 TTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCT-TCATC
1 TTCGATCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGT-AAA
* * *
1830 TTCGATCTGTTTCCCTACTGCTTAGGGAGATAAGATC--TACAA
1 TTCGATCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTA-AA
* * * * * ***
1872 TTCGATCTGTTACCCTACCGATTAGGGGTTTAAGACCTTTCGTC
1 TTCGATCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGT-AAA
* * *
1916 TTCGATCTGTTTCCCTACTACTTAGGGGGTTATGATCTGTAAA
1 TTCGATCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAA
** * * *
1959 TCTTTAGCCTGTTACCCTATTGCTTAGGGGCTTAAG
1 T-TCGA-TCTGTTACCCTACTGCTTAGGGGGTTAAG
1995 GCTTATGAAT
Statistics
Matches: 702, Mismatches: 156, Indels: 98
0.73 0.16 0.10
Matches are distributed among these distances:
41 2 0.00
42 65 0.09
43 273 0.39
44 190 0.27
45 172 0.25
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (43 bp):
TTCGATCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAA
Found at i:1229 original size:132 final size:131
Alignment explanation
Indices: 1093--1820 Score: 954
Period size: 132 Copynumber: 5.5 Consensus size: 131
1083 TAAATTCAAC
* * *
1093 CTGTTACCCTACTGGTTAGGGGGTTAAGATTTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGG
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGG
* * * *
1158 GGTTTAAGGTTTGTAAATTCGGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATTTTTT
66 GG-TTAAGGCTTGTAAATTTGGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTTG
1223 AT
130 AT
* * * *
1225 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTTAGTCAGTTACCCTACTTCTTAAG
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTT-AG
* *
1290 GGTTTAAGGCTTGTAAATTTGGCTTGTTACCCTACTGCTTAGTGGGTTAAAGCCCATCATCTTTG
65 GGGTTAAGGCTTGTAAATTTGGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTTG
1355 AT
130 AT
* *
1357 CTGTTTCCCTACTGCTTAAGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTACTTAGG
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGG
*
1422 GCGTTAAGGCTTGTAAATTTGGCTTGTTACCCTACTACTTAGGGGGTTAAAGCCCATCATCTTTG
66 G-GTTAAGGCTTGTAAATTTGGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTTG
1487 AT
130 AT
* * * * *
1489 CTATTTTCCTACTGCTTAGGGGGTTAAGATCT-T-CATCTTC-GATCTGTTTCCCTACTGCTTAG
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAG-CCTGTTACCCTACTGCTTAG
* * * ** *** * *
1551 GGAGATAA-GATCTG-CAATTCAG-TCTGTTACCCTACCAATTA-GGGGTTTAAGACCCTTCATC
65 GG-GTTAAGGCT-TGTAAATTTGGCT-TGTTACCCTACTGCTTAGGGGGTTAAAG-CCCATCATC
1612 TTTGAT
126 TTTGAT
1618 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGG
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTA-G
* **
1683 GGGTTAAGGCTTGTAAATTTAGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTCA
65 GGGTTAAGGCTTGTAAATTTGGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTTG
1748 AT
130 AT
* * *
1750 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCT-T-CATCTTC-GATCTGTTTCCCTACTGCTTAG
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAG-CCTGTTACCCTACTGCTTA-
1812 GGGGTTAAG
64 GGGGTTAAG
1821 ATCTTCATCT
Statistics
Matches: 524, Mismatches: 57, Indels: 32
0.85 0.09 0.05
Matches are distributed among these distances:
128 10 0.02
129 68 0.13
130 65 0.12
131 35 0.07
132 332 0.63
133 14 0.03
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (131 bp):
CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGG
GGTTAAGGCTTGTAAATTTGGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTTGA
T
Found at i:1320 original size:175 final size:176
Alignment explanation
Indices: 1007--1337 Score: 434
Period size: 175 Copynumber: 1.9 Consensus size: 176
997 ATTTCCAGCC
* *
1007 TGTTACCCTACTACTTAGGGGTTTAAGGCCCATCATCTTCGATCTATTTCCCAACTGCTTAAGGG
1 TGTTACCCTACTACTTAGGGGGTTAAAGCCCATCATCTTCGATCTATTTCCCAACTGCTTAAGGG
* * * *
1072 GTTAAGATCTGTAAATTCAACCTGTTACCCTACTGGTTAGGGGGTTAAGATTTGTAAATCTTCAG
66 GTTAAGATCTGTAAATTCAACCAGTTACCCTACTGCTTAAGGGGTTAAGACTTGTAAATCTTCAG
1137 CCTGTTACCCTACTGCTTAG-GGGTTTAAGGTTTGTAAATTCGGCT
131 CCTGTTACCCTACTGCTTAGTGGGTTTAAGGTTTGTAAATTCGGCT
* * ** * * *
1182 TGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATTTTTTATCTGTTTCCCTACTGCTTAGGGG
1 TGTTACCCTACTACTTAGGGGGTTAAAGCCCATCATCTTCGATCTATTTCCCAACTGCTTAAGGG
* ** * * *
1247 GTTAAGATCTGTAAATCTTTAGTCAGTTACCCTACTTCTTAAGGGTTTAAGGCTTGTAAAT-TT-
66 GTTAAGATCTGTAAA--TTCAACCAGTTACCCTACTGCTTAAGGGGTTAAGACTTGTAAATCTTC
* *
1310 GGCTTGTTACCCTACTGCTTAGTGGGTT
129 AGCCTGTTACCCTACTGCTTAGTGGGTT
1338 AAAGCCCATC
Statistics
Matches: 132, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
175 91 0.69
176 7 0.05
177 34 0.26
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.37
Consensus pattern (176 bp):
TGTTACCCTACTACTTAGGGGGTTAAAGCCCATCATCTTCGATCTATTTCCCAACTGCTTAAGGG
GTTAAGATCTGTAAATTCAACCAGTTACCCTACTGCTTAAGGGGTTAAGACTTGTAAATCTTCAG
CCTGTTACCCTACTGCTTAGTGGGTTTAAGGTTTGTAAATTCGGCT
Found at i:1788 original size:304 final size:305
Alignment explanation
Indices: 1446--1998 Score: 921
Period size: 304 Copynumber: 1.8 Consensus size: 305
1436 AAATTTGGCT
* * *
1446 TGTTACCCTACTACTTAGGGGGTTAAAGCCCATCATCTTTGATCTATTTTCCTACTGCTTAGGGG
1 TGTTACCCTACTACTTAGGGGGTTAAAGACCATCATCTTCGATCTATTTCCCTACTGCTTAGGGG
*
1511 GTTAAGATCTTCATCTTCGATCTGTTTCCCTACTGCTTAGGGAGATAAGATCTGCAATTC-AGTC
66 GTTAAGATCTTCATCTTCGATCTGTTTCCCTACTGCTTAGGGAGATAAGATCTACAATTCGA-TC
* *
1575 TGTTACCCTACCAATTAGGGGTTTAAGACCCTTCATCTTTGATCTGTTTCCCTACTGCTTAGGGG
130 TGTTACCCTACCAATTAGGGGTTTAAGACCCTTCATCTTCGATCTGTTTCCCTACTACTTAGGGG
*
1640 GTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTAAATTTAG
195 GTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGGGGCTTAAGGCTTGTAAATTTAG
1705 CTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTCAATC
260 CTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTCAATC
* * * * *
1751 TGTTTCCCTACTGCTTAGGGGGTT-AAGATCTTCATCTTCGATCTGTTTCCCTACTGCTTAGGGG
1 TGTTACCCTACTACTTAGGGGGTTAAAGACCATCATCTTCGATCTATTTCCCTACTGCTTAGGGG
1815 GTTAAGATCTTCATCTTCGATCTGTTTCCCTACTGCTTAGGGAGATAAGATCTACAATTCGATCT
66 GTTAAGATCTTCATCTTCGATCTGTTTCCCTACTGCTTAGGGAGATAAGATCTACAATTCGATCT
* * *
1880 GTTACCCTACCGATTAGGGGTTTAAGACCTTTCGTCTTCGATCTGTTTCCCTACTACTTAGGGGG
131 GTTACCCTACCAATTAGGGGTTTAAGACCCTTCATCTTCGATCTGTTTCCCTACTACTTAGGGGG
* * *
1945 TTATGATCTGTAAATCTTTAGCCTGTTACCCTATTGCTTAGGGGCTTAAGGCTT
196 TTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGGGGCTTAAGGCTT
1999 ATGAATTCAC
Statistics
Matches: 229, Mismatches: 18, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
304 206 0.90
305 23 0.10
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.37
Consensus pattern (305 bp):
TGTTACCCTACTACTTAGGGGGTTAAAGACCATCATCTTCGATCTATTTCCCTACTGCTTAGGGG
GTTAAGATCTTCATCTTCGATCTGTTTCCCTACTGCTTAGGGAGATAAGATCTACAATTCGATCT
GTTACCCTACCAATTAGGGGTTTAAGACCCTTCATCTTCGATCTGTTTCCCTACTACTTAGGGGG
TTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGGGGCTTAAGGCTTGTAAATTTAGC
TTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTCAATC
Found at i:1953 original size:86 final size:86
Alignment explanation
Indices: 1006--1953 Score: 558
Period size: 87 Copynumber: 10.9 Consensus size: 86
996 AATTTCCAGC
* * * * * * *
1006 CTGTTACCCTACTACTTAGGGGTTTAAGGCCCATCATCTTCGATCTATTTCCCAACTGCTTAAGG
1 CTGTTACCCTACTGCTTAGGGGGTTAA-GACCTTCATCTTCGATCTGTTTCCCTACTGCTTAGGG
** * * *
1071 GGTTAAGATCTGTAAATTCAAC
65 GGTTAAGATCTACATATTCGAT
* ** * * *
1093 CTGTTACCCTACTGGTTAGGGGGTTAAGATTTGTAAATCTTC-AGCCTGTTACCCTACTGCTTAG
1 CTGTTACCCTACTGCTTAGGGGGTTAAGACCT-T-CATCTTCGA-TCTGTTTCCCTACTGCTTAG
* * * ** * *
1157 GGGTTTAAGGTTTGTAAATTCG-G
63 GGGGTTAAGATCTACATATTCGAT
* * * **
1180 CTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATTTTTTATCTGTTTCCCTACTGCTTAGG
1 C-TGTTACCCTACTGCTTAGGGGGTT-AAGACCTTCATCTTCGATCTGTTTCCCTACTGCTTAGG
* * *
1245 GGGTTAAGATCTGTAAATCTT-TAGT
64 GGGTTAAGATC--TACATATTCGA-T
* * * * * * * * * * *
1270 CAGTTACCCTACTTCTTAAGGGTTTAAGGCTTGTAAAT-TTGGCT-TGTTACCCTACTGCTTAGT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGACCT-T-CATCTTCGATCTGTTTCCCTACTGCTTAGG
* * * *
1333 GGGTTAA-AGCCCATCATCTTTGAT
64 GGGTTAAGA-TCTA-CATATTCGAT
* * * * * * *
1357 CTGTTTCCCTACTGCTTAAGGGGTTAAGATCTGTAAATCTTC-AGCCTGTTACCCTACTACTTAG
1 CTGTTACCCTACTGCTTAGGGGGTTAAGACCT-T-CATCTTCGA-TCTGTTTCCCTACTGCTTAG
* * * * * *
1421 GGCGTTAAGGCTTGTAAAT-TTGGCT
63 GGGGTTAA-G-ATCTACATATTCGAT
* * * * * *
1446 -TGTTACCCTACTACTTAGGGGGTTAAAGCCCATCATCTTTGATCTATTTTCCTACTGCTTAGGG
1 CTGTTACCCTACTGCTTAGGGGGTT-AAGACCTTCATCTTCGATCTGTTTCCCTACTGCTTAGGG
* *
1510 GGTTAAGATCTTCATCTTCGAT
65 GGTTAAGATCTACATATTCGAT
* * * * * * * ***
1532 CTGTTTCCCTACTGCTTAGGGAGATAAGATCTGCA-ATTC-AGTCTGTTACCCTACCAATTAGGG
1 CTGTTACCCTACTGCTTAGGGGGTTAAGACCTTCATCTTCGA-TCTGTTTCCCTACTGCTTAGGG
* * * * *
1595 GTTTAAGACCCTTCATCTTTGAT
65 GGTTAAGA-TCTACATATTCGAT
* * * * *
1618 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTC-AGCCTGTTACCCTACTGCTTAG
1 CTGTTACCCTACTGCTTAGGGGGTTAAGACCT-T-CATCTTCGA-TCTGTTTCCCTACTGCTTAG
* * * * *
1682 GGGGTTAAGGCTTGTAAAT-TTAGCT
63 GGGGTTAA-G-ATCTACATATTCGAT
* * *
1707 -TGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTCAATCTGTTTCCCTACTGCTTAGGG
1 CTGTTACCCTACTGCTTAGGGGGTT-AAGACCTTCATCTTCGATCTGTTTCCCTACTGCTTAGGG
* *
1771 GGTTAAGATCTTCATCTTCGAT
65 GGTTAAGATCTACATATTCGAT
* * *
1793 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTCATCTTCGATCTGTTTCCCTACTGCTTAGGGA
1 CTGTTACCCTACTGCTTAGGGGGTTAAGACCTTCATCTTCGATCTGTTTCCCTACTGCTTAGGGG
*
1858 GATAAGATCTACA-ATTCGAT
66 GTTAAGATCTACATATTCGAT
* * * * *
1878 CTGTTACCCTACCGATTAGGGGTTTAAGACCTTTCGTCTTCGATCTGTTTCCCTACTACTTAGGG
1 CTGTTACCCTACTGCTTAGGGGGTTAAGACC-TTCATCTTCGATCTGTTTCCCTACTGCTTAGGG
*
1943 GGTTATGATCT
65 GGTTAAGATCT
1954 GTAAATCTTT
Statistics
Matches: 662, Mismatches: 162, Indels: 75
0.74 0.18 0.08
Matches are distributed among these distances:
84 1 0.00
85 65 0.10
86 145 0.22
87 198 0.30
88 145 0.22
89 98 0.15
90 9 0.01
91 1 0.00
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.37
Consensus pattern (86 bp):
CTGTTACCCTACTGCTTAGGGGGTTAAGACCTTCATCTTCGATCTGTTTCCCTACTGCTTAGGGG
GTTAAGATCTACATATTCGAT
Found at i:1974 original size:261 final size:261
Alignment explanation
Indices: 1006--1993 Score: 1043
Period size: 261 Copynumber: 3.8 Consensus size: 261
996 AATTTCCAGC
* * ** * * * *
1006 CTGTTACCCTACTACTTAGGGGTTTAAGGCCCATCATCTTCGATCTATTTCCCAACTGCTTAAGG
1 CTGTTACCCTACTGCTTAGGGGGTTAA-GATCTTCATCTTCGATCTGTTACCCTACTGCTT-AGG
** * * * *
1071 GGTTAAGATCTGTA-A-ATTCAACCTGTTACCCTACTGGTTAGGGGGTTAAGATTTGTAAATCTT
64 GGTTAAGA-CCCTACATATTCGATCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTT
* * * **
1134 CAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGTTTGTAAATTCGGCTTGTTACCCTACTGCTTA
128 CAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTGTAAATTTAGCTTGTTACCCTACTGCTTA
* * *
1199 GGGGGTTAAAGCCCATCATTTTTTATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATC
193 GGGGGTTAAAGCCCATCATCTTTAATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCT-T-CATC
*
1264 TT-TAGT
256 TTCGA-T
* * * * * * * *
1270 CAGTTACCCTACTTCTTAAGGGTTTAAG-GCTTGTAAAT-TTGGCT-TGTTACCCTACTGCTTAG
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATC-T-T-CATCTTCGATCTGTTACCCTACTGCTTAG
* * * *
1332 TGGGTTAA-AGCCC-ATCATCTTTGATCTGTTTCCCTACTGCTTAAGGGGTTAAGATCTGTAAAT
63 -GGGTTAAGA-CCCTA-CATATTCGATCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAAT
* * *
1395 CTTCAGCCTGTTACCCTACTACTTAGGGCGTTAAGGCTTGTAAATTTGGCTTGTTACCCTACTAC
125 CTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTGTAAATTTAGCTTGTTACCCTACTGC
* * *
1460 TTAGGGGGTTAAAGCCCATCATCTTTGATCTATTTTCCTACTGCTTAGGGGGTTAAGATCTTCAT
190 TTAGGGGGTTAAAGCCCATCATCTTTAATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTCAT
1525 CTTCGAT
255 CTTCGAT
* * * * * ***
1532 CTGTTTCCCTACTGCTTAGGGAGATAAGATCTGCA-ATTC-AGTCTGTTACCCTACCAATTAGGG
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTTCATCTTCGA-TCTGTTACCCTACTGCTTAGGG
* * * *
1595 GTTTAAGACCCTTCATCTTTGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTC
65 G-TTAAGACCCTACATATTCGATCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTC
*
1660 AGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTAAATTTAGCTTGTTACCCTACTGCTTAG
129 AGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTGTAAATTTAGCTTGTTACCCTACTGCTTAG
*
1725 GGGGTTAAAGCCCATCATCTTCAATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTCATCTTC
194 GGGGTTAAAGCCCATCATCTTTAATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTCATCTTC
1790 GAT
259 GAT
* *
1793 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTCATCTTCGATCTGTTTCCCTACTGCTTAGGGA
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTTCATCTTCGATCTGTTACCCTACTGCTTAGGG-
* * * * * * ***
1858 GATAAGA-TCTACA-ATTCGATCTGTTACCCTACCGATTAGGGGTTTAAGACCT-TTCGTCTTC-
65 GTTAAGACCCTACATATTCGATCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCA
* * * * * *
1919 GATCTGTTTCCCTACTACTTAGGGGGTT-ATGATCTGTAAATCTTTAGCCTGTTACCCTATTGCT
130 G-CCTGTTACCCTACTACTTAGGGGGTTAAGGCT-TGTAAA--TTTAGCTTGTTACCCTACTGCT
*
1983 TAGGGGCTTAA
191 TAGGGGGTTAA
1994 GGCTTATGAA
Statistics
Matches: 614, Mismatches: 88, Indels: 47
0.82 0.12 0.06
Matches are distributed among these distances:
258 4 0.01
259 35 0.06
260 39 0.06
261 265 0.43
262 60 0.10
263 27 0.04
264 182 0.30
265 2 0.00
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.37
Consensus pattern (261 bp):
CTGTTACCCTACTGCTTAGGGGGTTAAGATCTTCATCTTCGATCTGTTACCCTACTGCTTAGGGG
TTAAGACCCTACATATTCGATCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAG
CCTGTTACCCTACTACTTAGGGGGTTAAGGCTTGTAAATTTAGCTTGTTACCCTACTGCTTAGGG
GGTTAAAGCCCATCATCTTTAATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTCATCTTCGA
T
Found at i:2164 original size:66 final size:66
Alignment explanation
Indices: 2058--2184 Score: 209
Period size: 66 Copynumber: 1.9 Consensus size: 66
2048 TCTATGCTTA
* *
2058 TGTCAAATGATTAGGATGATATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGTTATGAAT
1 TGTCAAATAATTAGGATGATATGATCGAAATGAATCAAATGATCCTAACTAGATGTGTTATGAAT
2123 G
66 G
* * *
2124 TGTCAAATAATTAGGATGCTATGATTGAAATGAATCAAATGATCTTAACTAGATGTGTTAT
1 TGTCAAATAATTAGGATGATATGATCGAAATGAATCAAATGATCCTAACTAGATGTGTTAT
2185 TATATGAATG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 56 1.00
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.34
Consensus pattern (66 bp):
TGTCAAATAATTAGGATGATATGATCGAAATGAATCAAATGATCCTAACTAGATGTGTTATGAAT
G
Found at i:3375 original size:6 final size:6
Alignment explanation
Indices: 3364--3399 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
3354 TGTGTTTTTT
3364 TTTGCC TTTGCC TTTGCC TTTGCC TTTGCC TTTGCC
1 TTTGCC TTTGCC TTTGCC TTTGCC TTTGCC TTTGCC
3400 ATATAACTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.17, T:0.50
Consensus pattern (6 bp):
TTTGCC
Found at i:6212 original size:19 final size:20
Alignment explanation
Indices: 6188--6234 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
6178 AGTGAAAGTT
6188 TAATGCAAATGT-TGCAATG
1 TAATGCAAATGTATGCAATG
*
6207 TAATGCAAATGTATGGAATG
1 TAATGCAAATGTATGCAATG
6227 -AATGCAAA
1 TAATGCAAA
6235 AGAAAGGAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 20 0.77
20 6 0.23
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.28
Consensus pattern (20 bp):
TAATGCAAATGTATGCAATG
Done.