Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold6630.1
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: 10700
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Warning! 31 characters in sequence are not A, C, G, or T
Found at i:540 original size:75 final size:76
Alignment explanation
Indices: 420--620 Score: 257
Period size: 77 Copynumber: 2.6 Consensus size: 76
410 AAAGTAGATT
*
420 TTGAAAATACCTC-GACATGTGAACCCAAGGCTCAACTCACATCTCGCAATATGAGTTGA-TTTT
1 TTGAAAATAGCTCAG-CATGTG-ACCCAAGGCTCAACTCACATCTCGCAATATGAGTTGATTTTT
483 TGAAAAGCAGAAA
64 TGAAAAGCAGAAA
* * *
496 TT-AAAA-ACGCCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 TTGAAAATA-G-CTCAGCATGTGACCCAAGGCTCAACTCACATCTCGCAATATGAGTTGA-TTTT
559 TTGAAAAGCAGAAA
63 TTGAAAAGCAGAAA
* * * *
573 TTGAAAATAGCTCAGCACGTGAGCAAAGGCTCAACTCACTTCTCGCAA
1 TTGAAAATAGCTCAGCATGTGACCCAAGGCTCAACTCACATCTCGCAA
621 AAGTAGATTT
Statistics
Matches: 108, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
74 1 0.01
75 39 0.36
76 10 0.09
77 52 0.48
78 5 0.05
79 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.24
Consensus pattern (76 bp):
TTGAAAATAGCTCAGCATGTGACCCAAGGCTCAACTCACATCTCGCAATATGAGTTGATTTTTTG
AAAAGCAGAAA
Found at i:728 original size:14 final size:14
Alignment explanation
Indices: 692--742 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
682 GAGTTGATTT
* *
692 TTGAAAAATATAAA
1 TTGAAAAACAGAAA
706 TTGAAAAAAACAGAAA
1 TTG--AAAAACAGAAA
*
722 TTGAAAAGCAGAAA
1 TTGAAAAACAGAAA
736 TT-AAAAA
1 TTGAAAAA
743 GACCTCAGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 4 0.13
14 15 0.48
16 12 0.39
ACGTcount: A:0.65, C:0.04, G:0.12, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:889 original size:14 final size:14
Alignment explanation
Indices: 870--919 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
860 GAGTTAATTT
* *
870 TTGAAAAATATAAA
1 TTGAAAAACAGAAA
884 TTGAAAAAACAGAAA
1 TTG-AAAAACAGAAA
*
899 TTGAAAAGCAGAAA
1 TTGAAAAACAGAAA
913 TT-AAAAA
1 TTGAAAAA
920 GACCTCAGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 4 0.13
14 15 0.48
15 12 0.39
ACGTcount: A:0.64, C:0.04, G:0.12, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:954 original size:177 final size:181
Alignment explanation
Indices: 652--1071 Score: 686
Period size: 177 Copynumber: 2.3 Consensus size: 181
642 CGACATGTGA
* *
652 ACCCAAGGCTCAACTCACATCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAAAAAAC
1 ACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGAAAAATATAAATTG-AAAAAAC
717 AGAAATTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCAC
65 AGAAATTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCAC
* *
782 AATATGAGTT-A-ATTTTTGACAAATAGAAATTG-AAATTACCTCAGCGTGT
130 AATATGAGTTGATATTTTTGACAAACAGAAATTGAAAAATACCTCAGCGTGT
* *
831 -CCCGAGGCTCAACTCACCTTTCGCAATATGAGTTAATTTTTGAAAAATATAAATTGAAAAAACA
1 ACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGAAAAATATAAATTGAAAAAACA
895 GAAATTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCACA
66 GAAATTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCACA
*
960 ATATGAGTTGATTTTTTTGACAAACAGAAATTGAAAAATACCTCAGCGTGT
131 ATATGAGTTGATATTTTTGACAAACAGAAATTGAAAAATACCTCAGCGTGT
* * * * *
1011 AAGCCAAGGCTCAACTCACCTCTCGCAATATGTGTTAATTTTTGACAAACAGAAATTGAAA
1 -ACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGAAAAATATAAATTGAAA
1072 TTACCTCAGC
Statistics
Matches: 222, Mismatches: 14, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
177 82 0.37
178 53 0.24
179 19 0.09
180 16 0.07
182 52 0.23
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.25
Consensus pattern (181 bp):
ACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGAAAAATATAAATTGAAAAAACA
GAAATTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCACA
ATATGAGTTGATATTTTTGACAAACAGAAATTGAAAAATACCTCAGCGTGT
Found at i:1113 original size:73 final size:75
Alignment explanation
Indices: 899--1221 Score: 382
Period size: 76 Copynumber: 4.3 Consensus size: 75
889 AAAACAGAAA
* * ** * *
899 TTGA-AAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCACAATA
1 TTGACAAA-CAGAAATTGAAAATACCTCAGC--GTGTCCCGAGGCTCAACTCACCTCTCGCAATA
*
963 TGAGTTGATTTTT
63 TGAGTTGATATTT
* *
976 TTGACAAACAGAAATTGAAAAATACCTCAGCGTGTAAGCCAAGGCTCAACTCACCTCTCGCAATA
1 TTGACAAACAGAAATTG-AAAATACCTCAGCGTGT--CCCGAGGCTCAACTCACCTCTCGCAATA
*
1041 TGTGTT-A-ATTT
63 TGAGTTGATATTT
* *
1052 TTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTTTCGCAATATGA
1 TTGACAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
*
1117 GTTGATTTTT
66 GTTGATATTT
* * * *
1127 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAAGCTCAACTCACCTCTCGCAATATG
1 TTGACAAACAGAAA-TTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATG
*
1192 AGTTGATTTTT
65 AGTTGATATTT
* *
1203 TTTACGAACAGAAATTGAA
1 TTGACAAACAGAAATTGAA
1222 GAACAGAAAT
Statistics
Matches: 215, Mismatches: 24, Indels: 16
0.84 0.09 0.06
Matches are distributed among these distances:
73 30 0.14
74 1 0.00
75 36 0.17
76 90 0.42
77 13 0.06
78 45 0.21
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (75 bp):
TTGACAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATATTT
Found at i:1213 original size:151 final size:152
Alignment explanation
Indices: 921--1366 Score: 467
Period size: 151 Copynumber: 2.8 Consensus size: 152
911 AATTAAAAAG
* * *
921 ACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCACAATATGAGTTGATTTTTTTGACAAACA
1 ACCTCAGCA-GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACA
* * *
986 GAAATTGAAAAATACCTCAGCGTGTAAGCC-AAGGCTCAACTCACCTCTCGCAATATGTGTTA-A
65 GAAATTTAAAAATACCTCAGCGTGT---CCGAA-GCTCAACTCACCTCTCGCAATATGAGTTATT
1049 TTTTTGACAAACAGAAATT-GAAATT-
126 TTTTTGACAAACAGAAATTAGAAATTA
* * *
1074 ACCTCAGC-GTGTCCCGAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTTTGAAAAACAG
1 ACCTCAGCAGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACAG
1138 AAATTTAAAAATACCTCAGCGTGTCCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
66 AAATTTAAAAATACCTCAGCGTGTCC-GAAGCTCAACTCACCTCTCGCAATATGAGTT-ATTTTT
* *
1203 TTTACGAACAGAAATTGAAGAACAGAAATTGAAAA
129 TTGACAAACAGAAATT-------AGAAATT----A
** * *
1238 GACCTCAGCATGTGAGTCGAGGCTCAACTCACCTCTCGCAATATGTGTT-A-ATTTTTGACAAAC
1 -ACCTCAGCA-GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAAC
* * * * *
1301 AGAAA-TTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTTTCGCAATATGAGTTAATTT
64 AGAAATTTAAAAATACCTCAGCGTGT-CCGAAGCTCAACTCACCTCTCGCAATATGAGTTATTTT
1365 TT
128 TT
1367 GAAAAATATA
Statistics
Matches: 249, Mismatches: 23, Indels: 32
0.82 0.08 0.11
Matches are distributed among these distances:
148 2 0.01
149 27 0.11
150 3 0.01
151 90 0.36
153 8 0.03
159 6 0.02
163 6 0.02
164 47 0.19
165 26 0.10
166 1 0.00
167 33 0.13
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.29
Consensus pattern (152 bp):
ACCTCAGCAGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACAG
AAATTTAAAAATACCTCAGCGTGTCCGAAGCTCAACTCACCTCTCGCAATATGAGTTATTTTTTT
GACAAACAGAAATTAGAAATTA
Found at i:1227 original size:14 final size:14
Alignment explanation
Indices: 1208--1235 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1198 TTTTTTTTAC
1208 GAACAGAAATTGAA
1 GAACAGAAATTGAA
1222 GAACAGAAATTGAA
1 GAACAGAAATTGAA
1236 AAGACCTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
GAACAGAAATTGAA
Found at i:1350 original size:73 final size:74
Alignment explanation
Indices: 1217--1385 Score: 223
Period size: 73 Copynumber: 2.3 Consensus size: 74
1207 CGAACAGAAA
* **
1217 TTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGTCGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTGAAAAGACCTCAGCA-GTGACCCGAGGCTCAACTCACCTCTCGCAATAT
*
1282 GTGTTAATTT
65 GAGTTAATTT
* ** * *
1292 TTGACAAACAGAAATTGAAATTACCTCAGC-GTGTCCCGAGGCTCAACTCACCTTTCGCAATATG
1 TTGAAAAACAGAAATTGAAAAGACCTCAGCAGTGACCCGAGGCTCAACTCACCTCTCGCAATATG
1356 AGTTAATTT
66 AGTTAATTT
* *
1365 TTGAAAAATATAAATTGAAAA
1 TTGAAAAACAGAAATTGAAAA
1386 AACAGAAATT
Statistics
Matches: 81, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
73 55 0.68
75 26 0.32
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (74 bp):
TTGAAAAACAGAAATTGAAAAGACCTCAGCAGTGACCCGAGGCTCAACTCACCTCTCGCAATATG
AGTTAATTT
Found at i:1384 original size:14 final size:14
Alignment explanation
Indices: 1365--1414 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
1355 GAGTTAATTT
* *
1365 TTGAAAAATATAAA
1 TTGAAAAACAGAAA
1379 TTGAAAAAACAGAAA
1 TTG-AAAAACAGAAA
*
1394 TTGAAAAGCAGAAA
1 TTGAAAAACAGAAA
1408 TT-AAAAA
1 TTGAAAAA
1415 GACCTCAGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 4 0.13
14 15 0.48
15 12 0.39
ACGTcount: A:0.64, C:0.04, G:0.12, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:1435 original size:495 final size:491
Alignment explanation
Indices: 714--1633 Score: 1628
Period size: 495 Copynumber: 1.9 Consensus size: 491
704 AATTGAAAAA
714 AACAGAAATTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCT
1 AACAGAAATTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCT
*
779 CACAATATGAGTTAATTTTTGACAAATAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAAC
66 CACAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAAC
844 TCACCTTTCGCAATATGAGTTAATTTTTGAAAAATATAAATTGAAAAAACAGAAATTGAAAAGCA
131 TCACCTTTCGCAATATGAGTTAATTTTTGAAAAATATAAATTGAAAAAACAGAAATTGAAAAGCA
909 GAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCACAATATGAGTTGATTT
196 GAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCACAATATGAGTTGATTT
974 TTTTGACAAACAGAAATTGAAAAATACCTCAGCGTGTAAGCCAAGGCTCAACTCACCTCTCGCAA
261 TTTTGACAAACAGAAATTGAAAAATACCTCAGCGTGTAAGCCAAGGCTCAACTCACCTCTCGCAA
* * ** *
1039 TATGTGTT-AATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCAC
326 TATGAGTTGAATTTTTGAAAAACAGAAATTGAAAACACCTCAGCATGT---GAGGCTCAACTCAC
*
1103 CTTTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAA
388 CTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAA
1168 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTACG
451 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTACG
* * *
1209 AACAGAAATTGAAGAA-CAGAAATTGAAAAGACCTCAGCATGTGAGTCGAGGCTCAACTCACCTC
1 AACAGAAATTGAA-AAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTC
* *
1273 TCGCAATATGTGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAA
65 TCACAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAA
1338 CTCACCTTTCGCAATATGAGTTAATTTTTGAAAAATATAAATTGAAAAAACAGAAATTGAAAAGC
130 CTCACCTTTCGCAATATGAGTTAATTTTTGAAAAATATAAATTGAAAAAACAGAAATTGAAAAGC
1403 AGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCACAATATGAGTTGATT
195 AGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCACAATATGAGTTGATT
1468 TTTTTGACAAACAGAAATTGAAAAATACCTCAGCGTGTAAGCCAAGGCTCAACTCACCTCTCGCA
260 TTTTTGACAAACAGAAATTGAAAAATACCTCAGCGTGTAAGCCAAGGCTCAACTCACCTCTCGCA
* * *
1533 ATATGAGTTGATTTTTTGAAAAATAGAAATTGAAAACACTTCAGCATGTGAGGCTCAACTCACCT
325 ATATGAGTTGAATTTTTGAAAAACAGAAATTGAAAACACCTCAGCATGTGAGGCTCAACTCACCT
*
1598 CTCGCAATATGAGTTGATTTTTGAAAAACATAAATT
390 CTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT
1634 GAGCAGAAAT
Statistics
Matches: 407, Mismatches: 16, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
491 18 0.04
493 32 0.08
495 323 0.79
496 34 0.08
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (491 bp):
AACAGAAATTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCT
CACAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAAC
TCACCTTTCGCAATATGAGTTAATTTTTGAAAAATATAAATTGAAAAAACAGAAATTGAAAAGCA
GAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCACAATATGAGTTGATTT
TTTTGACAAACAGAAATTGAAAAATACCTCAGCGTGTAAGCCAAGGCTCAACTCACCTCTCGCAA
TATGAGTTGAATTTTTGAAAAACAGAAATTGAAAACACCTCAGCATGTGAGGCTCAACTCACCTC
TCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAAGCTCA
ACTCACCTCTCGCAATATGAGTTGATTTTTTTTACG
Found at i:1524 original size:78 final size:75
Alignment explanation
Indices: 1394--1635 Score: 307
Period size: 78 Copynumber: 3.2 Consensus size: 75
1384 AAAACAGAAA
* * * *
1394 TTGAAAAGCAGAAATT-AAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCACAATA
1 TTGAAAAACAGAAATTGAAAAACACCTCAGCATGT-AGCC-AGGCTCAACTCACCTCTCGCAATA
1458 TGAGTTGATTTTT
64 TGAGTTGA-TTTT
* * *
1471 TTGACAAACAGAAATTGAAAAATACCTCAGCGTGTAAGCCAAGGCTCAACTCACCTCTCGCAATA
1 TTGAAAAACAGAAATTGAAAAACACCTCAGCATGT-AGCC-AGGCTCAACTCACCTCTCGCAATA
1536 TGAGTTGATTTT
64 TGAGTTGATTTT
* *
1548 TTGAAAAATAGAAATTG-AAAACACTTCAGCATGT-G--AGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTGAAAAACACCTCAGCATGTAGCCAGGCTCAACTCACCTCTCGCAATATG
1609 AGTTGA-TTT
66 AGTTGATTTT
*
1618 TTGAAAAACATAAATTGA
1 TTGAAAAACAGAAATTGA
1636 GCAGAAATTG
Statistics
Matches: 148, Mismatches: 15, Indels: 10
0.86 0.09 0.06
Matches are distributed among these distances:
70 18 0.12
71 32 0.22
74 1 0.01
76 14 0.09
77 33 0.22
78 50 0.34
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (75 bp):
TTGAAAAACAGAAATTGAAAAACACCTCAGCATGTAGCCAGGCTCAACTCACCTCTCGCAATATG
AGTTGATTTT
Found at i:1706 original size:155 final size:158
Alignment explanation
Indices: 1516--1883 Score: 439
Period size: 155 Copynumber: 2.3 Consensus size: 158
1506 AAGCCAAGGC
*
1516 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAGAAATTGAAAACACTTC-A-G-C
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAAT--AAATTGAAAACACCTCAATGTC
* * *
1578 A-TGTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG-A-AAAACATAAATTG-AGC
64 ACT-TGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTGAATAAAACAGAAATTGAAAC
* * * *
1638 AGAAATTGAAAATACCTCAACGGGTCTTGAGGT
128 AGAAATGGAAAACACCTC-A-GCGTATTGAGGT
** * *
1671 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTG-ATGATAAATTGAAAATACCTCAATGTGAC
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAAATTGAAAACACCTCAATGTCAC
* *
1735 TTGAGGTTCAACTCACCTCTCACAATATGAGTTGATTTTTTGAATTAAAACAGAAATTGAAAATA
66 TTGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTGAA-TAAAACAGAAATTG-AAACA
1800 GAAATGGAAAACACCTCAGCGTATTGAGGT
129 GAAATGGAAAACACCTCAGCGTATTGAGGT
* *
1830 TCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAACACATAAATTAAAAA
1 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAA-A-ATAAATTGAAAA
1884 AAAAAGAAAT
Statistics
Matches: 181, Mismatches: 18, Indels: 20
0.83 0.08 0.09
Matches are distributed among these distances:
152 14 0.08
153 1 0.01
154 4 0.02
155 68 0.38
156 7 0.04
157 1 0.01
159 49 0.27
160 8 0.04
161 18 0.10
163 11 0.06
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (158 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAAATTGAAAACACCTCAATGTCAC
TTGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTGAATAAAACAGAAATTGAAACAGA
AATGGAAAACACCTCAGCGTATTGAGGT
Found at i:1761 original size:71 final size:71
Alignment explanation
Indices: 1640--1777 Score: 240
Period size: 71 Copynumber: 1.9 Consensus size: 71
1630 AATTGAGCAG
* *
1640 AAATTGAAAATACCTCAACGGGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAACGGGACTTGAGGTTCAACTCACCTCTCACAATATGAGTTGATTTTTT
1705 GATGAT
66 GATGAT
* *
1711 AAATTGAAAATACCTCAATGTGACTTGAGGTTCAACTCACCTCTCACAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAACGGGACTTGAGGTTCAACTCACCTCTCACAATATGAGTTGATTTTTT
1776 GA
66 GA
1778 ATTAAAACAG
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 63 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (71 bp):
AAATTGAAAATACCTCAACGGGACTTGAGGTTCAACTCACCTCTCACAATATGAGTTGATTTTTT
GATGAT
Found at i:2070 original size:75 final size:76
Alignment explanation
Indices: 1894--2076 Score: 230
Period size: 75 Copynumber: 2.4 Consensus size: 76
1884 AAAAAGAAAT
1894 TAAAAACAGAATTTGAAAGGACCTC-GACGTGTGGCCCGAGACTCAACTCACCTCTCGCAATATG
1 TAAAAACAGAATTTGAAA-GACCTCAG-CGTGT-GCCCGAGACTCAACTCACCTCTCGCAATATG
1958 AGTTGATTCTTTTA
63 AGTTGATTCTTTTA
* * * * *
1972 -AAAAGCAAAAATTGAAAATACCTCAGCGTGT-CCCGAGGCTCAACTCACCTCTCGCAATATGAG
1 TAAAAACAGAATTTG-AAAGACCTCAGCGTGTGCCCGAGACTCAACTCACCTCTCGCAATATGAG
*
2035 TTGATTTTTTTGA
65 TTGATTCTTTT-A
*
2048 TAAAAATAGAATTTGAAA-ACCTCAGCGTG
1 TAAAAACAGAATTTGAAAGACCTCAGCGTG
2077 NNNNNNNNNN
Statistics
Matches: 91, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
75 52 0.57
76 4 0.04
77 31 0.34
78 4 0.04
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (76 bp):
TAAAAACAGAATTTGAAAGACCTCAGCGTGTGCCCGAGACTCAACTCACCTCTCGCAATATGAGT
TGATTCTTTTA
Found at i:2225 original size:72 final size:74
Alignment explanation
Indices: 2108--2253 Score: 251
Period size: 72 Copynumber: 2.0 Consensus size: 74
2098 NNNNNNNNNN
2108 TACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTG-AAAACAAA
1 TACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATATTTTGAAAAACAAA
2171 AATTGAAAT
66 AATTGAAAT
* *
2180 TACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTGAAAAACAG
1 TACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TATTTTGAAAAACAA
2245 AAATTGAAA
65 AAATTGAAA
2254 GGCTTAATTG
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
72 49 0.71
74 5 0.07
75 15 0.22
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Consensus pattern (74 bp):
TACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATATTTTGAAAAACAAA
AATTGAAAT
Found at i:2510 original size:73 final size:71
Alignment explanation
Indices: 2417--2611 Score: 248
Period size: 72 Copynumber: 2.7 Consensus size: 71
2407 ATTAAAAGGT
* * * * *
2417 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAATTACCTCATCGTGT
1 TCAACTCACCTCTCGCAATATGAGTTGATT-TTGA-AAACAAAAATTGAAAATACCTCAGCGTGC
*
2482 CCTGAGGC
64 CCCGAGGC
* * *
2490 TCAACTCACCTCTCACAATATGAGTTGATATTAGAACACAAAAATTGAAAATACCTCAGCGTGCC
1 TCAACTCACCTCTCGCAATATGAGTTGAT-TTTGAAAACAAAAATTGAAAATACCTCAGCGTGCC
2555 CCGAGGC
65 CCGAGGC
* *
2562 TCAACTCACCTCTCGCAATATGGGCTGATTTTGAAAAACAAAAATT-AAAA
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTG-AAAACAAAAATTGAAAA
2612 GGCTTAACTC
Statistics
Matches: 106, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
71 7 0.07
72 68 0.64
73 30 0.28
74 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (71 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTGAAAATACCTCAGCGTGCCC
CGAGGC
Found at i:2714 original size:122 final size:124
Alignment explanation
Indices: 2486--2732 Score: 349
Period size: 122 Copynumber: 2.0 Consensus size: 124
2476 TCGTGTCCTG
** * *
2486 AGGCTCAACTCACCTCTCACAATATGAGTTGATATTAGAACACAAAAATTGAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCACAATATGAGTCAATATTAGAACACAAAAACTAAAAATACCTCAGCG
2551 TGCCCCGAGGCTCAACTCACCTCTCGCAATATGGGCTGATTTTGAAAAACAAAAATTAAA
66 TGCCCCGAGGCTCAACTCACCTCTCGCAATATGGGCTGATTTTG-AAAACAAAAATTAAA
* * * *
2611 AGGCTTAACTCACCTCTCGCAATATGAGTCAAT-TTA-AA-ACATAAACTAAAAATACCTCGGCG
1 AGGCTCAACTCACCTCTCACAATATGAGTCAATATTAGAACACAAAAACTAAAAATACCTCAGCG
* * *
2673 TGCCCCGAGGCTCAACTCACTTCTCGCAATATGAG-TCGATTTTGTAAACAAAAATTAAA
66 TGCCCCGAGGCTCAACTCACCTCTCGCAATATGGGCT-GATTTTGAAAACAAAAATTAAA
2732 A
1 A
2733 ATACCTCATC
Statistics
Matches: 110, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
121 16 0.15
122 60 0.55
123 2 0.02
124 3 0.03
125 29 0.26
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (124 bp):
AGGCTCAACTCACCTCTCACAATATGAGTCAATATTAGAACACAAAAACTAAAAATACCTCAGCG
TGCCCCGAGGCTCAACTCACCTCTCGCAATATGGGCTGATTTTGAAAACAAAAATTAAA
Found at i:2755 original size:71 final size:70
Alignment explanation
Indices: 2611--2786 Score: 212
Period size: 71 Copynumber: 2.5 Consensus size: 70
2601 AAAAATTAAA
* * * * *
2611 AGGCTTAACTCACCTCTCGCAATATGAGTC-AATTTAAAACATAAACTAAAAATACCTCGGCGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTCGATTTTAAAACAAAAACTAAAAATACCTCAGCGTG
2675 CCCCG
66 CCCCG
* * *
2680 AGGCTCAACTCACTTCTCGCAATATGAGTCGATTTTGTAAACAAAAATTAAAAATACCTCATCGT
1 AGGCTCAACTCACTTCTCGCAATATGAGTCGATTTT-AAAACAAAAACTAAAAATACCTCAGCGT
* **
2745 GTCTTG
65 GCCCCG
*
2751 AGGCTCAACTCA-TCTCTCGCAATATGAGTTGATTTT
1 AGGCTCAACTCACT-TCTCGCAATATGAGTCGATTTT
2787 CCTTGAAAAG
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
69 28 0.30
70 5 0.05
71 59 0.64
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (70 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTCGATTTTAAAACAAAAACTAAAAATACCTCAGCGTG
CCCCG
Found at i:2786 original size:193 final size:198
Alignment explanation
Indices: 2264--2786 Score: 673
Period size: 199 Copynumber: 2.6 Consensus size: 198
2254 GGCTTAATTG
* * **
2264 AAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAATTGAAATTAAAACA
1 AAAATACCTCGGC--GTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTGAACA
2329 CAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTT
63 CAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTT
* * * *
2394 TGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGACAAACAG
128 TGAAAAAGCAAAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTCAATCTTGACAAACAG
* *
2459 AAATTG
193 AAACTA
* ** * * *
2465 AAATTACCTCATCGTGTCCTGAGGCTCAACTCACCTCTCACAATATGAGTTGATATTAGAACACA
1 AAAATACCTCGGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT-TTTGAACACA
*
2530 AAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGGGCTGATTTTG
65 AAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTG
* *
2595 AAAAA-CAAAAATTAAAAGGCTT-AACTCACCTCTCGCAATATGAG-TCAAT-TT-A-AAACATA
130 AAAAAGCAAAAATTAAAAGG-TTCAACCCACCTCTCGCAATATGAGTTCAATCTTGACAAACAGA
2654 AACTA
194 AACTA
* * * *
2659 AAAATACCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTCGATTTTGTAA-ACA
1 AAAATACCTCGGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTG-AACACA
* * * ** * *
2723 AAAATTAAAAATACCTCATCGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTT
65 AAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTT
2787 CCTTGAAAAG
Statistics
Matches: 285, Mismatches: 34, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
193 62 0.22
194 57 0.20
195 1 0.00
196 2 0.01
197 3 0.01
198 34 0.12
199 116 0.41
201 10 0.04
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.26
Consensus pattern (198 bp):
AAAATACCTCGGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAACACAA
AAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTGA
AAAAGCAAAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTCAATCTTGACAAACAGAAA
CTA
Done.