Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1843
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: 52442
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1168 original size:20 final size:19
Alignment explanation
Indices: 1145--1225 Score: 92
Period size: 20 Copynumber: 4.1 Consensus size: 19
1135 TTTTTGTTGC
1145 TGTTGTTTTTGTT-TTTTTTT
1 TGTT-TTTTT-TTCTTTTTTT
*
1165 TGTTTTTTTTCTCTTGTTTGT
1 TGTTTTTTTT-TCTT-TTTTT
*
1186 TGTTTTTTTTCCTTCTTTTT
1 TGTTTTTTTTTCTT-TTTTT
1206 TGTTTTTTTTTCTTTTTTT
1 TGTTTTTTTTTCTTTTTTT
1225 T
1 T
1226 TCTTCCTCTT
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
18 1 0.02
19 12 0.23
20 26 0.49
21 14 0.26
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.83
Consensus pattern (19 bp):
TGTTTTTTTTTCTTTTTTT
Found at i:1181 original size:14 final size:12
Alignment explanation
Indices: 1150--1226 Score: 61
Period size: 12 Copynumber: 6.1 Consensus size: 12
1140 GTTGCTGTTG
1150 TTTTTG-TTTTT
1 TTTTTGTTTTTT
1161 TTTTTGTTTTTT
1 TTTTTGTTTTTT
1173 TTCTCTTGTTTGTTGT
1 TT-T-TTGTTT-TT-T
*
1189 TTTTT-TTCCTTCT
1 TTTTTGTT--TTTT
1202 TTTTTGTTTTTT
1 TTTTTGTTTTTT
1214 TTTCTT-TTTTTT
1 TTT-TTGTTTTTT
1226 T
1 T
1227 CTTCCTCTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
11 6 0.11
12 20 0.36
13 11 0.20
14 11 0.20
15 4 0.07
16 3 0.05
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.84
Consensus pattern (12 bp):
TTTTTGTTTTTT
Found at i:1205 original size:32 final size:31
Alignment explanation
Indices: 1188--1260 Score: 51
Period size: 33 Copynumber: 2.3 Consensus size: 31
1178 TTGTTTGTTG
* * *
1188 TTTTTTTTCCTTCTTTTTTGTTTTTTTTTCTTT
1 TTTTTTTT-CTTCTTTCTT-TTTTTTTTCCTTC
*
1221 TTTTTTCTTCCTCTTT-TTTTTCTTCTTT-CTTC
1 TTTTTT-TTCTTCTTTCTTTTT-TT-TTTCCTTC
1253 TTTTTTTT
1 TTTTTTTT
1261 TGTGGAGGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
31 5 0.14
32 13 0.37
33 15 0.43
34 2 0.06
ACGTcount: A:0.00, C:0.16, G:0.01, T:0.82
Consensus pattern (31 bp):
TTTTTTTTCTTCTTTCTTTTTTTTTTCCTTC
Found at i:1226 original size:20 final size:20
Alignment explanation
Indices: 1157--1226 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
1147 TTGTTTTTGT
1157 TTTTTTTTTGTTTTTTTTCTC
1 TTTTTTTTTGTTTTTTTT-TC
* * *
1178 TTGTTTGTTGTTTTTTTTCC
1 TTTTTTTTTGTTTTTTTTTC
*
1198 TTCTTTTTTGTTTTTTTTTC
1 TTTTTTTTTGTTTTTTTTTC
1218 TTTTTTTTT
1 TTTTTTTTT
1227 CTTCCTCTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
20 26 0.62
21 16 0.38
ACGTcount: A:0.00, C:0.09, G:0.07, T:0.84
Consensus pattern (20 bp):
TTTTTTTTTGTTTTTTTTTC
Found at i:1253 original size:52 final size:52
Alignment explanation
Indices: 1150--1258 Score: 136
Period size: 52 Copynumber: 2.1 Consensus size: 52
1140 GTTGCTGTTG
* *
1150 TTTTTGTTTTTTTTTTGTTTTTTTTCTCTTGTTTGTTGTTTTTTTTCCTTCT
1 TTTTTGTTTTTTTTTTGTTTTTTTTCTCCTCTTTGTTGTTTTTTTTCCTTCT
1202 TTTTTGTTTTTTTTTCT-TTTTTTTTCTTCCTCTTT-TT-TTTCTTCTTT-CTTCT
1 TTTTTGTTTTTTTTT-TGTTTTTTTTC-TCCTCTTTGTTGTTT-TT-TTTCCTTCT
1254 TTTTT
1 TTTTT
1259 TTTGTGGAGG
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
51 3 0.06
52 38 0.75
53 10 0.20
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.82
Consensus pattern (52 bp):
TTTTTGTTTTTTTTTTGTTTTTTTTCTCCTCTTTGTTGTTTTTTTTCCTTCT
Found at i:9197 original size:31 final size:32
Alignment explanation
Indices: 9145--9237 Score: 134
Period size: 32 Copynumber: 2.9 Consensus size: 32
9135 TTCAACGATT
*
9145 TGTATTGATACATAAAGTGTTGTATCGATACAA
1 TGTATTCATACAT-AAGTGTTGTATCGATACAA
9178 TGTA-TCATACATAAGTGTTGTATCGATACAA
1 TGTATTCATACATAAGTGTTGTATCGATACAA
* * *
9209 TGTATTGATACATAAGTTTTGTATTGATA
1 TGTATTCATACATAAGTGTTGTATCGATA
9238 AGATACTGCC
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
31 23 0.42
32 28 0.51
33 4 0.07
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (32 bp):
TGTATTCATACATAAGTGTTGTATCGATACAA
Found at i:9351 original size:52 final size:52
Alignment explanation
Indices: 9308--9436 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
9298 CACTGATCTT
*
9308 TGTATCGATATATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* * *
9360 TGTATCGATACATACAGGCAAATTTGTCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
9412 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
9437 TCATATTTCG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:17830 original size:20 final size:20
Alignment explanation
Indices: 17807--17853 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
17797 AAAGGTGCTG
**
17807 AACATGCTGTAAATGCATGA
1 AACATGCTCAAAATGCATGA
17827 AACATAGCTCAAAATGCATGA
1 AACAT-GCTCAAAATGCATGA
*
17848 ATCATG
1 AACATG
17854 GACTGTTATC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (20 bp):
AACATGCTCAAAATGCATGA
Found at i:18790 original size:52 final size:52
Alignment explanation
Indices: 18641--18769 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
18631 CGAAATATGA
18641 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
18693 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
18745 AAATTTGCCTGCATGAATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
18770 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:18866 original size:19 final size:18
Alignment explanation
Indices: 18842--18938 Score: 88
Period size: 19 Copynumber: 5.8 Consensus size: 18
18832 AACTGTACAT
18842 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
18861 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
18874 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
18893 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
*
18906 CGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
18925 TGTATCGATACAAA
1 TGTATCGATACAAA
18939 TCGTTGAAAT
Statistics
Matches: 64, Mismatches: 2, Indels: 25
0.70 0.02 0.27
Matches are distributed among these distances:
13 21 0.33
14 2 0.03
16 4 0.06
18 3 0.05
19 34 0.53
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:18878 original size:32 final size:32
Alignment explanation
Indices: 18837--18936 Score: 182
Period size: 32 Copynumber: 3.1 Consensus size: 32
18827 TTCGTAACTG
*
18837 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
18869 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
*
18901 TACATCGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
18933 TACA
1 TACA
18937 AATCGTTGAA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 66 1.00
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:18879 original size:13 final size:13
Alignment explanation
Indices: 18861--18917 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
18851 ACAAAACTTA
18861 TGTATCGATACAT
1 TGTATCGATACAT
18874 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
18892 ATGTATCGATACAT
1 -TGTATCGATACAT
*
18906 CGTATCGATACA
1 TGTATCGATACA
18918 ACACTTATGT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 20 0.54
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:20736 original size:81 final size:81
Alignment explanation
Indices: 20616--21192 Score: 638
Period size: 81 Copynumber: 7.2 Consensus size: 81
20606 CACTATCGAA
* * **
20616 GATACTCCAACCCCATCATTTTCGAGGGGATACTTCAACCTTGTTTTTACTTCTAAAAATATCAA
1 GATACTCCAACCCCACCATTTTCGAGGGGATACTCCAACCCCGTTTTTACTTCTAAAAATATCAA
20681 ATTTTTCATCTTAGGG
66 ATTTTTCATCTTAGGG
* *
20697 GATACTCCAACCCCACCATTTTCGAGGGGATAATCCAACCCCGTTTTTACTCCTAAAAATATCAA
1 GATACTCCAACCCCACCATTTTCGAGGGGATACTCCAACCCCGTTTTTACTTCTAAAAATATCAA
*
20762 ATTTTTCATCTTCGGG
66 ATTTTTCATCTTAGGG
* * * * *
20778 GATACTCCAACCCTACCATTTTCAAGGGGATACTTC-A-----TTTTTACTCCTAAAAATACCAA
1 GATACTCCAACCCCACCATTTTCGAGGGGATACTCCAACCCCGTTTTTACTTCTAAAAATATCAA
* *
20837 AATTTTCATCTTCGGG
66 ATTTTTCATCTTAGGG
* * * * *
20853 GATACTCCAA-CCTACCATTTTCGAGGGGATACTCGAAGCCCATTTTTTC-TCTTAAAAATATCA
1 GATACTCCAACCCCACCATTTTCGAGGGGATACTCCAACCCCGTTTTTACTTC-TAAAAATATCA
20916 AATTTTTCATCTT-GAGG
65 AATTTTTCATCTTAG-GG
* * * **
20933 GATACTCCAACCGCACCATTTTCGAGAGGATACTCCAACCCCATTTTTACTTCTAAACGTATCAA
1 GATACTCCAACCCCACCATTTTCGAGGGGATACTCCAACCCCGTTTTTACTTCTAAAAATATCAA
* *
20998 ACTTTTCATCTTCGGG
66 ATTTTTCATCTTAGGG
* * * * * * *
21014 GATACTCCAACCCCATCATTTTTGAGAGGATACTCTAATCCTGTTTTTACTTCAACAAAAATATC
1 GATACTCCAACCCCACCATTTTCGAGGGGATACTCCAACCCCGTTTTTACTTC--TAAAAATATC
* *
21079 AAATTTTCCATCTTCA-AG
64 AAATTTTTCATCTT-AGGG
** * * *
21097 GATACTCCAACCCCAGTATTTCCGAGGGGATAGTCCAACCCCATTTTTACTTCTAAAAATATCAA
1 GATACTCCAACCCCACCATTTTCGAGGGGATACTCCAACCCCGTTTTTACTTCTAAAAATATCAA
21162 A-TTTTCTATCTTA-GG
66 ATTTTTC-ATCTTAGGG
* *
21177 GATACTCTAATCCCAC
1 GATACTCCAACCCCAC
21193 TATCTCTGAA
Statistics
Matches: 422, Mismatches: 59, Indels: 31
0.82 0.12 0.06
Matches are distributed among these distances:
74 22 0.05
75 47 0.11
79 2 0.00
80 60 0.14
81 225 0.53
82 3 0.01
83 63 0.15
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (81 bp):
GATACTCCAACCCCACCATTTTCGAGGGGATACTCCAACCCCGTTTTTACTTCTAAAAATATCAA
ATTTTTCATCTTAGGG
Found at i:21047 original size:236 final size:237
Alignment explanation
Indices: 20616--21192 Score: 672
Period size: 236 Copynumber: 2.4 Consensus size: 237
20606 CACTATCGAA
* *
20616 GATACTCCAACCCCATCATTTTCGAGGGGATACTTCAA-CCTTGTTTTTACTTCTAAAAATATCA
1 GATACTCCAA--CCACCATTTTCGAGGGGATAC-TCAACCCAT-TTTTT-CTTCTAAAAATATCA
* *
20680 AATTTTTCATCTTAGGGGATACTCCAACCCCACCATTTTCGAGGGGATAATCCAACCCCGTTTTT
61 AATTTTTCATCTTA-GGGATACTCCAACCCCACCATTTTCGAGAGGATAATCCAACCCCATTTTT
* * *
20745 ACTCCTAAAAATATCAAATTTTTCATCTTCGGGGATACTCCAACCCTACCATTTTCAAGGGGATA
125 ACTCCTAAAAATATCAAACTTTTCATCTTCGGGGATACTCCAACCCCACCATTTTCAAGAGGATA
**
20810 -CT-T-C-ATTTTTAC-TC-CTAAAAATACCAAAATTTT-CATCTTCGGG
190 CCTATCCTATTTTTACTTCAC-AAAAATACC-AAATTTTCCATCTTCAAG
20853 GATACTCCAACCTACCATTTTCGAGGGGATACTCGAAGCCCATTTTTTC-TCTTAAAAATATCAA
1 GATACTCCAACC-ACCATTTTCGAGGGGATACTC-AA-CCCATTTTTTCTTC-TAAAAATATCAA
* *
20917 ATTTTTCATCTTGAGGGATACTCCAACCGCACCATTTTCGAGAGGATACTCCAACCCCATTTTTA
62 ATTTTTCATCTT-AGGGATACTCCAACCCCACCATTTTCGAGAGGATAATCCAACCCCATTTTTA
* ** * **
20982 CTTCTAAACGTATCAAACTTTTCATCTTCGGGGATACTCCAACCCCATCATTTTTGAGAGGATAC
126 CTCCTAAAAATATCAAACTTTTCATCTTCGGGGATACTCCAACCCCACCATTTTCAAGAGGATAC
* *
21047 TCTAATCCTGTTTTTACTTCAACAAAAATATCAAATTTTCCATCTTCAAG
191 -CT-ATCCTATTTTTACTTC-ACAAAAATACCAAATTTTCCATCTTCAAG
* *
21097 GATACTCCAACC-CCAGTATTTCCGAGGGGATAGTCCAACCCCATTTTTACTTCTAAAAATATCA
1 GATACTCCAACCACCA-T-TTT-CGAGGGGATACT-CAA-CCCATTTTTTCTTCTAAAAATATCA
* *
21161 AA-TTTTCTATCTTAGGGATACTCTAATCCCAC
61 AATTTTTC-ATCTTAGGGATACTCCAACCCCAC
21193 TATCTCTGAA
Statistics
Matches: 293, Mismatches: 25, Indels: 37
0.83 0.07 0.10
Matches are distributed among these distances:
235 6 0.02
236 147 0.50
237 16 0.05
238 5 0.02
240 1 0.00
241 1 0.00
242 10 0.03
243 10 0.03
244 52 0.18
245 42 0.14
246 3 0.01
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (237 bp):
GATACTCCAACCACCATTTTCGAGGGGATACTCAACCCATTTTTTCTTCTAAAAATATCAAATTT
TTCATCTTAGGGATACTCCAACCCCACCATTTTCGAGAGGATAATCCAACCCCATTTTTACTCCT
AAAAATATCAAACTTTTCATCTTCGGGGATACTCCAACCCCACCATTTTCAAGAGGATACCTATC
CTATTTTTACTTCACAAAAATACCAAATTTTCCATCTTCAAG
Found at i:24494 original size:97 final size:97
Alignment explanation
Indices: 24328--24513 Score: 264
Period size: 97 Copynumber: 1.9 Consensus size: 97
24318 TTGATTGAAA
* * *
24328 AATGGGGTTGGAGTGTCCCCGATGATGACAATTTAAGTGAAAATAAGATTTAAGCTTTGATACAT
1 AATGGAGTTGAAGTGTCCCCGATGATGACAATTTAAGTGAAAATAAGATTTAAACTTTGATACAT
** *
24393 TTAAAAATGGGGTTGGAGTATCCCCTCGGAGG
66 TTAAAAACAGGGTTGAAGTATCCCCTCGGAGG
* * ***
24425 AATGGAGTTGAAGTGTCCCCGATGGTGACAATTTAAGTGAGAATAAGATTTAAACTTTGATGTGT
1 AATGGAGTTGAAGTGTCCCCGATGATGACAATTTAAGTGAAAATAAGATTTAAACTTTGATACAT
*
24490 TTAAAAGCAGGGTTGAAGTATCCC
66 TTAAAAACAGGGTTGAAGTATCCC
24514 TCAAAGGAAT
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
97 77 1.00
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.30
Consensus pattern (97 bp):
AATGGAGTTGAAGTGTCCCCGATGATGACAATTTAAGTGAAAATAAGATTTAAACTTTGATACAT
TTAAAAACAGGGTTGAAGTATCCCCTCGGAGG
Found at i:26255 original size:12 final size:11
Alignment explanation
Indices: 26191--26258 Score: 55
Period size: 12 Copynumber: 5.7 Consensus size: 11
26181 GCTATCCTTA
26191 TTTTTTTTCTACC
1 TTTTTTTTCT--C
* *
26204 TCTTTGTTTCTA
1 T-TTTTTTTCTC
*
26216 TTTCTTTTCTC
1 TTTTTTTTCTC
*
26227 TTTTCTTTCTC
1 TTTTTTTTCTC
26238 TTTTTTTTTCTC
1 -TTTTTTTTCTC
26250 TCTTTTTTT
1 T-TTTTTTT
26259 TTTGTCTTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
11 17 0.39
12 18 0.41
13 1 0.02
14 8 0.18
ACGTcount: A:0.03, C:0.21, G:0.01, T:0.75
Consensus pattern (11 bp):
TTTTTTTTCTC
Found at i:26255 original size:13 final size:13
Alignment explanation
Indices: 26223--26272 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
26213 CTATTTCTTT
*
26223 TCTCTTTTCTTTC
1 TCTCTTTTTTTTC
26236 TCT-TTTTTTTTC
1 TCTCTTTTTTTTC
*
26248 TCTCTTTTTTTTT
1 TCTCTTTTTTTTC
*
26261 TGTCTTTTTTTT
1 TCTCTTTTTTTT
26273 AGTTGAACCT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
12 11 0.33
13 22 0.67
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (13 bp):
TCTCTTTTTTTTC
Found at i:27672 original size:37 final size:37
Alignment explanation
Indices: 27622--27712 Score: 182
Period size: 37 Copynumber: 2.5 Consensus size: 37
27612 ATGGGTTTGT
27622 CCTCCATACCAAGTTACTAAAAATCTCTAAGGCTTGA
1 CCTCCATACCAAGTTACTAAAAATCTCTAAGGCTTGA
27659 CCTCCATACCAAGTTACTAAAAATCTCTAAGGCTTGA
1 CCTCCATACCAAGTTACTAAAAATCTCTAAGGCTTGA
27696 CCTCCATACCAAGTTAC
1 CCTCCATACCAAGTTAC
27713 CAAGTTCTGG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.34, C:0.30, G:0.10, T:0.26
Consensus pattern (37 bp):
CCTCCATACCAAGTTACTAAAAATCTCTAAGGCTTGA
Found at i:27848 original size:31 final size:32
Alignment explanation
Indices: 27788--27875 Score: 110
Period size: 31 Copynumber: 2.8 Consensus size: 32
27778 GACATAGGTA
* **
27788 CCACCAACTTGTGTGGGTTTTGACTAGGG-TG
1 CCACCAACTTGTGTGGGCTTTGAAAAGGGTTG
27819 CCACCAACTTGTGTGGGCTTTGAAAAGGGTTG
1 CCACCAACTTGTGTGGGCTTTGAAAAGGGTTG
**
27851 CCACTGAC-T-TGTGGGCTTTGAAAAG
1 CCACCAACTTGTGTGGGCTTTGAAAAG
27876 TTTCCATTGA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
30 16 0.31
31 27 0.53
32 8 0.16
ACGTcount: A:0.20, C:0.19, G:0.31, T:0.30
Consensus pattern (32 bp):
CCACCAACTTGTGTGGGCTTTGAAAAGGGTTG
Found at i:28199 original size:28 final size:28
Alignment explanation
Indices: 27830--28238 Score: 418
Period size: 28 Copynumber: 14.5 Consensus size: 28
27820 CACCAACTTG
*
27830 TGTGGGCTTTGAAAAGGGTTGCCACTGACT
1 TGTGGGCTTTGAAAA--GATGCCACTGACT
* * *
27860 TGTGGGCTTTGAAAAGTTTCCATTGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* * *
27888 T-TTGGCTTTTAAATATG-TGCCATTGACT
1 TGTGGGCTTTGAAA-A-GATGCCACTGACT
** * *
27916 TGTTAGCTTTTG-AAAGGTGCCATTGACT
1 TGTGGGC-TTTGAAAAGATGCCACTGACT
* * *
27944 TATTGGCTTTTG-AAAGGTGCCACTGACT
1 TGTGGGC-TTTGAAAAGATGCCACTGACT
* * *
27972 TGTGGGCTTTG-AAAGGTGCCACTAAAT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* *
27999 TGTGTGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
28027 TGTGGGCTTTTGAAAAGATGCCACTGACT
1 TGTGGGC-TTTGAAAAGATGCCACTGACT
* *
28056 TGTGGGCTTTGAAATGATGCCATTGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
*
28084 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* * *
28112 TATGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* * *
28140 TATGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
*
28168 TGTGGGCTTTTGAAAAGATGCCACTAAC-
1 TGTGGGC-TTTGAAAAGATGCCACTGACT
*
28196 TGTGGGCTTTAAAAAGAATGCCACTGACT
1 TGTGGGCTTTGAAAAG-ATGCCACTGACT
28225 TGTGGGC-TTGAAAA
1 TGTGGGCTTTGAAAA
28239 AGGGTTGTAT
Statistics
Matches: 337, Mismatches: 32, Indels: 22
0.86 0.08 0.06
Matches are distributed among these distances:
27 47 0.14
28 212 0.63
29 60 0.18
30 18 0.05
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (28 bp):
TGTGGGCTTTGAAAAGATGCCACTGACT
Found at i:29542 original size:19 final size:18
Alignment explanation
Indices: 29520--29605 Score: 74
Period size: 19 Copynumber: 4.9 Consensus size: 18
29510 TAGACCCCTA
29520 TTTTTTGTGTTTTTCTATT
1 TTTTTTGTGTTTTT-TATT
*
29539 TTTTTTTTGTTTTTTATT
1 TTTTTTGTGTTTTTTATT
* *
29557 TTCTTTTAT-TTTTTT-TG
1 TT-TTTTGTGTTTTTTATT
*
29574 TTTTTTAT-TTTTTT-TGT
1 TTTTTTGTGTTTTTTAT-T
29591 TTTTTTGT-TTTTTTA
1 TTTTTTGTGTTTTTTA
29606 AGAATGATGC
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
16 13 0.22
17 16 0.27
18 12 0.20
19 18 0.31
ACGTcount: A:0.06, C:0.02, G:0.07, T:0.85
Consensus pattern (18 bp):
TTTTTTGTGTTTTTTATT
Found at i:29551 original size:8 final size:8
Alignment explanation
Indices: 29540--29604 Score: 71
Period size: 8 Copynumber: 7.9 Consensus size: 8
29530 TTTTCTATTT
29540 TTTTTTTG
1 TTTTTTTG
29548 TTTTTTAT-
1 TTTTTT-TG
*
29556 TTTCTTTTAT
1 TTT-TTTT-G
29566 TTTTTTTG
1 TTTTTTTG
29574 TTTTTTAT-
1 TTTTTT-TG
29582 TTTTTTTG
1 TTTTTTTG
29590 TTTTTTTG
1 TTTTTTTG
29598 TTTTTTT
1 TTTTTTT
29605 AAGAATGATG
Statistics
Matches: 50, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
7 1 0.02
8 37 0.74
9 9 0.18
10 3 0.06
ACGTcount: A:0.05, C:0.02, G:0.06, T:0.88
Consensus pattern (8 bp):
TTTTTTTG
Found at i:29558 original size:25 final size:24
Alignment explanation
Indices: 29530--29603 Score: 105
Period size: 26 Copynumber: 3.0 Consensus size: 24
29520 TTTTTTGTGT
29530 TTTTCTATTTTTTTTTTGTTTTTTA
1 TTTTCT-TTTTTTTTTTGTTTTTTA
29555 TTTTCTTTTATTTTTTTTGTTTTTTA
1 TTTTC-TTT-TTTTTTTTGTTTTTTA
29581 TTTT-TTTTGTTTTTTTGTTTTTT
1 TTTTCTTTT-TTTTTTTGTTTTTT
29604 TAAGAATGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
23 1 0.02
24 17 0.37
25 7 0.15
26 21 0.46
ACGTcount: A:0.05, C:0.03, G:0.05, T:0.86
Consensus pattern (24 bp):
TTTTCTTTTTTTTTTTGTTTTTTA
Found at i:29569 original size:45 final size:43
Alignment explanation
Indices: 29518--29601 Score: 123
Period size: 45 Copynumber: 1.9 Consensus size: 43
29508 TCTAGACCCC
*
29518 TATTTTTTGTGTTTTTCTATTTTTTTTTTGTTTTTTATTTTCTTT
1 TATTTTTTGTGTTTTT-TATTTTTTTTGT-TTTTTTATTTTCTTT
* *
29563 TATTTTTTTTGTTTTTTATTTTTTTTGTTTTTTTGTTTT
1 TATTTTTTGTGTTTTTTATTTTTTTTGTTTTTTTATTTT
29602 TTTAAGAATG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 10 0.28
44 11 0.31
45 15 0.42
ACGTcount: A:0.06, C:0.02, G:0.07, T:0.85
Consensus pattern (43 bp):
TATTTTTTGTGTTTTTTATTTTTTTTGTTTTTTTATTTTCTTT
Found at i:29604 original size:26 final size:26
Alignment explanation
Indices: 29530--29605 Score: 93
Period size: 25 Copynumber: 3.0 Consensus size: 26
29520 TTTTTTGTGT
* *
29530 TTTTCTATT-TTTTTTTTGTTTTTTA
1 TTTTCTTTTATTTTTTTTTTTTTTTA
*
29555 TTTTCTTTTATTTTTTTTGTTTTTTA
1 TTTTCTTTTATTTTTTTTTTTTTTTA
* *
29581 TTTT-TTTTGTTTTTTTGTTTTTTTA
1 TTTTCTTTTATTTTTTTTTTTTTTTA
29606 AGAATGATGC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
25 26 0.57
26 20 0.43
ACGTcount: A:0.07, C:0.03, G:0.05, T:0.86
Consensus pattern (26 bp):
TTTTCTTTTATTTTTTTTTTTTTTTA
Found at i:29621 original size:1 final size:1
Alignment explanation
Indices: 29537--29604 Score: 64
Period size: 1 Copynumber: 68.0 Consensus size: 1
29527 TGTTTTTCTA
* * * * * * * *
29537 TTTTTTTTTTGTTTTTTATTTTCTTTTATTTTTTTTGTTTTTTATTTTTTTTGTTTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
29602 TTT
1 TTT
29605 AAGAATGATG
Statistics
Matches: 51, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.04, C:0.01, G:0.06, T:0.88
Consensus pattern (1 bp):
T
Found at i:41297 original size:97 final size:97
Alignment explanation
Indices: 41180--41366 Score: 320
Period size: 97 Copynumber: 1.9 Consensus size: 97
41170 AAAAACTGGA
* *
41180 TTGGAGTATCCCCTCAGAGGAATGGGGTTGGAGTGTCCCCGATGATGACAATTTAAGTGAGAATA
1 TTGGAGTATCCCCTCAGAGGAATGGGGTTGAAATGTCCCCGATGATGACAATTTAAGTGAGAATA
*
41245 AGATTTAAACTTTGATGCGTTTAAAAGCAGGG
66 AGATTTAAACTTTAATGCGTTTAAAAGCAGGG
* * *
41277 TTGGAGTATCCCTTCGGAGGAATGGGGTTGAAATGTCCCCGATGGTGACAATTTAAGTGAGAATA
1 TTGGAGTATCCCCTCAGAGGAATGGGGTTGAAATGTCCCCGATGATGACAATTTAAGTGAGAATA
41342 AGATTTAAACTTTAATGCGTTTAAA
66 AGATTTAAACTTTAATGCGTTTAAA
41367 CTTTGAGTGA
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
97 84 1.00
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.29
Consensus pattern (97 bp):
TTGGAGTATCCCCTCAGAGGAATGGGGTTGAAATGTCCCCGATGATGACAATTTAAGTGAGAATA
AGATTTAAACTTTAATGCGTTTAAAAGCAGGG
Found at i:41511 original size:70 final size:70
Alignment explanation
Indices: 41417--41571 Score: 238
Period size: 70 Copynumber: 2.2 Consensus size: 70
41407 GGAGGAATGA
* *
41417 GGTTGAAGTGTCCCCGATGATGACAATTTAAATGAAAATAAGATTTAAACTTTGATGCATTTAAA
1 GGTTGGAGTATCCCCGATGATGACAATTTAAATGAAAATAAGATTTAAACTTTGATGCATTTAAA
41482 AGCAG
66 AGCAG
* * * * *
41487 GGTTGGAGTATCCTCGATGGTGACAATTTAAGTGAGAATAAGATTTAAACTTTGATGCGTTTAAA
1 GGTTGGAGTATCCCCGATGATGACAATTTAAATGAAAATAAGATTTAAACTTTGATGCATTTAAA
*
41552 AGCGG
66 AGCAG
41557 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
41572 TCGGAGGAAT
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
70 76 1.00
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (70 bp):
GGTTGGAGTATCCCCGATGATGACAATTTAAATGAAAATAAGATTTAAACTTTGATGCATTTAAA
AGCAG
Found at i:43429 original size:13 final size:11
Alignment explanation
Indices: 43340--43427 Score: 95
Period size: 11 Copynumber: 7.7 Consensus size: 11
43330 ACTAGCCTTA
43340 TTTTTTTTCTACC
1 TTTTTTTTCT--C
* *
43353 TCTTTGTTTCTA
1 T-TTTTTTTCTC
*
43365 TTTCTTTTCTC
1 TTTTTTTTCTC
* *
43376 TTTTCTTTCTT
1 TTTTTTTTCTC
43387 TTTTTTTTCTC
1 TTTTTTTTCTC
*
43398 TTTTTATTCTC
1 TTTTTTTTCTC
43409 TTTTTTTTCTC
1 TTTTTTTTCTC
43420 TTTTTTTT
1 TTTTTTTT
43428 TTATTTGAGC
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
11 52 0.84
12 1 0.02
13 1 0.02
14 8 0.13
ACGTcount: A:0.03, C:0.18, G:0.01, T:0.77
Consensus pattern (11 bp):
TTTTTTTTCTC
Done.