Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1604
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: 83405
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:6251 original size:19 final size:19
Alignment explanation
Indices: 6229--6289 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
6219 AACAAATTCA
6229 AGATTTGCTTAAAAATAAG
1 AGATTTGCTTAAAAATAAG
*
6248 AGATTTG-TGT--GAA-AAG
1 AGATTTGCT-TAAAAATAAG
*
6264 ATATTTGCTTAAAAATAAG
1 AGATTTGCTTAAAAATAAG
6283 AGATTTG
1 AGATTTG
6290 TGTGAAAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
16 10 0.30
17 3 0.09
18 3 0.09
19 17 0.52
ACGTcount: A:0.43, C:0.03, G:0.20, T:0.34
Consensus pattern (19 bp):
AGATTTGCTTAAAAATAAG
Found at i:6272 original size:35 final size:35
Alignment explanation
Indices: 6231--6300 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
6221 CAAATTCAAG
6231 ATTTGCTTAAAAATAAGAGATTTGTGTGAAAAGAT
1 ATTTGCTTAAAAATAAGAGATTTGTGTGAAAAGAT
6266 ATTTGCTTAAAAATAAGAGATTTGTGTGAAAAGAT
1 ATTTGCTTAAAAATAAGAGATTTGTGTGAAAAGAT
6301 TTTAGAGTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.43, C:0.03, G:0.20, T:0.34
Consensus pattern (35 bp):
ATTTGCTTAAAAATAAGAGATTTGTGTGAAAAGAT
Found at i:6297 original size:19 final size:19
Alignment explanation
Indices: 6240--6297 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
6230 GATTTGCTTA
6240 AAAATAAGAGATTTGTGTG
1 AAAATAAGAGATTTGTGTG
* *
6259 --AA-AAGATATTTGCT-TA
1 AAAATAAGAGATTTG-TGTG
6275 AAAATAAGAGATTTGTGTG
1 AAAATAAGAGATTTGTGTG
6294 AAAA
1 AAAA
6298 GATTTTAGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
16 10 0.33
17 3 0.10
18 3 0.10
19 14 0.47
ACGTcount: A:0.47, C:0.02, G:0.21, T:0.31
Consensus pattern (19 bp):
AAAATAAGAGATTTGTGTG
Found at i:7117 original size:70 final size:70
Alignment explanation
Indices: 7034--7176 Score: 259
Period size: 70 Copynumber: 2.0 Consensus size: 70
7024 TGAATAAGTA
*
7034 TAAATGATATTAATACTATACTTAGGCCAATCCCATGAGCTTCTAGTTGGAAGACATCTTTGGAC
1 TAAATGATATTAATACTATACTTAGGCCAACCCCATGAGCTTCTAGTTGGAAGACATCTTTGGAC
7099 TATTT
66 TATTT
* *
7104 TAAATGATATTAATCCTATACTTAGGCCAACCCCATGAGCTTCTAGTTGGAAGACATTTTTGGAC
1 TAAATGATATTAATACTATACTTAGGCCAACCCCATGAGCTTCTAGTTGGAAGACATCTTTGGAC
7169 TATTT
66 TATTT
7174 TAA
1 TAA
7177 CTTAGTAATT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.36
Consensus pattern (70 bp):
TAAATGATATTAATACTATACTTAGGCCAACCCCATGAGCTTCTAGTTGGAAGACATCTTTGGAC
TATTT
Found at i:12073 original size:187 final size:187
Alignment explanation
Indices: 11758--12132 Score: 723
Period size: 187 Copynumber: 2.0 Consensus size: 187
11748 CCGTTGTTGA
11758 CTTGTTTGGTGCTTGTTTCCATGCATTCCCGTTAGTATGCATCGATACTTTTCATAATGTATCGA
1 CTTGTTTGGTGCTTGTTTCCATGCATTCCCGTTAGTATGCATCGATACTTTTCATAATGTATCGA
11823 TACATGCATTTGAAATTTATAGCCGTTAGGACAATGTATCGATACTTTTCATTATGTATCAATAA
66 TACATGCATTTGAAATTTATAGCCGTTAGGACAATGTATCGATACTTTTCATTATGTATCAATAA
*
11888 AATGTACTACGTATCGATACAAACAATGGTAGGGTAGCTATTGCCAGTTTCATGTAT
131 AATGTACTACGTATCGATACAAACAATGGTAGGGTAGCTACTGCCAGTTTCATGTAT
11945 CTTGTTTGGTGCTTGTTTCCATGCATTCCCGTTAGTATGCATCGATACTTTTCATAATGTATCGA
1 CTTGTTTGGTGCTTGTTTCCATGCATTCCCGTTAGTATGCATCGATACTTTTCATAATGTATCGA
*
12010 TACATGCATTTGAAATTTATAGCCGTTAGGACAATGTATCGATACTTTTCATTATTTATCAATAA
66 TACATGCATTTGAAATTTATAGCCGTTAGGACAATGTATCGATACTTTTCATTATGTATCAATAA
*
12075 AATGTACTACGTATCGATACAAATAATGGTAGGGTAGCTACTGCCAGTTTCATGTAT
131 AATGTACTACGTATCGATACAAACAATGGTAGGGTAGCTACTGCCAGTTTCATGTAT
12132 C
1 C
12133 GATACAATTG
Statistics
Matches: 185, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
187 185 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (187 bp):
CTTGTTTGGTGCTTGTTTCCATGCATTCCCGTTAGTATGCATCGATACTTTTCATAATGTATCGA
TACATGCATTTGAAATTTATAGCCGTTAGGACAATGTATCGATACTTTTCATTATGTATCAATAA
AATGTACTACGTATCGATACAAACAATGGTAGGGTAGCTACTGCCAGTTTCATGTAT
Found at i:12189 original size:20 final size:19
Alignment explanation
Indices: 12126--12195 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 19
12116 TGCCAGTTTC
12126 ATGTATCGATACAATT-GAGT
1 ATGTATCGATAC-ATTGGA-T
** *
12146 ATGTATCGATACAAAGCAT
1 ATGTATCGATACATTGGAT
12165 AATGTATCGATACATCTGGAT
1 -ATGTATCGATACAT-TGGAT
12186 ATGTATCGAT
1 ATGTATCGAT
12196 TCTTTCTAGG
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
19 2 0.05
20 36 0.88
21 3 0.07
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.33
Consensus pattern (19 bp):
ATGTATCGATACATTGGAT
Found at i:17078 original size:55 final size:55
Alignment explanation
Indices: 16975--17090 Score: 144
Period size: 56 Copynumber: 2.1 Consensus size: 55
16965 ACCCAAAATG
* * * ** *
16975 GGCATCTATAATAAAAAGAAATAAAAAACAAAAAAAATGGATGAAAACCTGAGAAA
1 GGCATCCAAAATAAAAAGAAACAAAAAACAAAAAAAATAAATGAAAACCT-AAAAA
* *
17031 GGCATCCAAAATAAAAGGAAACAAAAAACAAAAAAATTAAATG-AAACCTAAAAA
1 GGCATCCAAAATAAAAAGAAACAAAAAACAAAAAAAATAAATGAAAACCTAAAAA
17085 GGCATC
1 GGCATC
17091 TAATCCAAGA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
54 10 0.19
55 6 0.12
56 36 0.69
ACGTcount: A:0.62, C:0.12, G:0.13, T:0.13
Consensus pattern (55 bp):
GGCATCCAAAATAAAAAGAAACAAAAAACAAAAAAAATAAATGAAAACCTAAAAA
Found at i:18500 original size:66 final size:64
Alignment explanation
Indices: 18428--18570 Score: 173
Period size: 66 Copynumber: 2.2 Consensus size: 64
18418 AGTTGGTTTG
* ** * *
18428 TATGGTTTCGTCTCGATTAACCCTTTTTCAACTTAGGTTTCACTTT-GCTCATCCAAAGTT-AGT
1 TATGGTTTCGTCCCGACCAACCCTTTTT-AACTCAAGTTTCACTTTAG-TCA-CCAAAGTTGA-T
18491 TCA
62 TCA
*
18494 TATGGTTTCGTCCCGGCCAACCCTTTTTAACTCAAGTTTCACTTTAGTCACCAAAGTTGATTCA
1 TATGGTTTCGTCCCGACCAACCCTTTTTAACTCAAGTTTCACTTTAGTCACCAAAGTTGATTCA
*
18558 TATGGTTTTGTCC
1 TATGGTTTCGTCC
18571 TGGTCAACTC
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
64 24 0.35
65 19 0.28
66 25 0.37
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.41
Consensus pattern (64 bp):
TATGGTTTCGTCCCGACCAACCCTTTTTAACTCAAGTTTCACTTTAGTCACCAAAGTTGATTCA
Found at i:20105 original size:12 final size:13
Alignment explanation
Indices: 20083--20107 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20073 TTTCTACTTT
20083 GTAAAATTTTTTG
1 GTAAAATTTTTTG
20096 GTAAAATTTTTT
1 GTAAAATTTTTT
20108 TAGGTTTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
GTAAAATTTTTTG
Found at i:20153 original size:22 final size:19
Alignment explanation
Indices: 20113--20154 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
20103 TTTTTTAGGT
20113 TTAAAATTTTTAAAATTCA
1 TTAAAATTTTTAAAATTCA
20132 TTAAATATTTTTATTAAATTCA
1 TTAAA-ATTTTTA--AAATTCA
20154 T
1 T
20155 GTTAAATCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 7 0.35
22 8 0.40
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (19 bp):
TTAAAATTTTTAAAATTCA
Found at i:23350 original size:21 final size:20
Alignment explanation
Indices: 23300--23352 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
23290 TAAAAATTTG
*
23300 TCTCCCCTTTTAATAAAATT
1 TCTCCCCTTTTAATAAAATC
*
23320 TCTTCTCCTTTTCAA-AAACATC
1 TC-TCCCCTTTT-AATAAA-ATC
23342 TCTCCCCTTTT
1 TCTCCCCTTTT
23353 TGTTTCTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
20 2 0.07
21 19 0.70
22 6 0.22
ACGTcount: A:0.23, C:0.32, G:0.00, T:0.45
Consensus pattern (20 bp):
TCTCCCCTTTTAATAAAATC
Found at i:25534 original size:30 final size:29
Alignment explanation
Indices: 25498--25603 Score: 88
Period size: 30 Copynumber: 3.5 Consensus size: 29
25488 CATGGCTCAT
25498 TGTATCGATACATTCTGAGTTTTACCGAGA
1 TGTATCGATACATTCT-AGTTTTACCGAGA
* * * *
25528 TGTATCGATACATTGTTCA-TTGTATCGATACA
1 TGTATCGATACATT-CT-AGTTTTACCG--AGA
* * *
25560 TTATATCGATACATTCTAGGTTTACCCAGA
1 -TGTATCGATACATTCTAGTTTTACCGAGA
25590 TGTATCGATACATT
1 TGTATCGATACATT
25604 TTTCAATGTA
Statistics
Matches: 58, Mismatches: 13, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
29 13 0.22
30 22 0.38
31 3 0.05
32 7 0.12
33 13 0.22
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (29 bp):
TGTATCGATACATTCTAGTTTTACCGAGA
Found at i:25566 original size:13 final size:13
Alignment explanation
Indices: 25545--25574 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
25535 ATACATTGTT
*
25545 CATTGTATCGATA
1 CATTATATCGATA
25558 CATTATATCGATA
1 CATTATATCGATA
25571 CATT
1 CATT
25575 CTAGGTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (13 bp):
CATTATATCGATA
Found at i:25598 original size:62 final size:63
Alignment explanation
Indices: 25495--25623 Score: 206
Period size: 62 Copynumber: 2.1 Consensus size: 63
25485 ATACATGGCT
* * * *
25495 CATTGTATCGATACATTCTGAGTTTTACCGAGATGTATCGATACATTGTTCATTGTATCGATA
1 CATTATATCGATACATTCTGAGGTTTACCCAGATGTATCGATACATTGTTCAATGTATCGATA
*
25558 CATTATATCGATACATTCT-AGGTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATA
1 CATTATATCGATACATTCTGAGGTTTACCCAGATGTATCGATACATTGTTCAATGTATCGATA
25620 CATT
1 CATT
25624 CAGGCATTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
62 43 0.70
63 18 0.30
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.40
Consensus pattern (63 bp):
CATTATATCGATACATTCTGAGGTTTACCCAGATGTATCGATACATTGTTCAATGTATCGATA
Found at i:27867 original size:50 final size:49
Alignment explanation
Indices: 27813--27938 Score: 146
Period size: 50 Copynumber: 2.5 Consensus size: 49
27803 TAAATTTCTA
* * * *
27813 GATTTTTCATCTCAGGGATACTCCAACCCCTGCTTTATTTCTAAAATATT
1 GATTTTTCATCTCAGGGATACTCCAA-CCCAGCTTTATTTCCAAAACATC
* *
27863 GATTTTTCATCTC-GGGAATACTCTAACCCAGTTTTATTTCCAAAACATC
1 GATTTTTCATCTCAGGG-ATACTCCAACCCAGCTTTATTTCCAAAACATC
* *
27912 AATTTTTCATAATCAGGGATACTCCAA
1 GATTTTTCAT-CTCAGGGATACTCCAA
27939 TCCCGTTATT
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
49 30 0.47
50 31 0.48
51 3 0.05
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.37
Consensus pattern (49 bp):
GATTTTTCATCTCAGGGATACTCCAACCCAGCTTTATTTCCAAAACATC
Found at i:27918 original size:49 final size:50
Alignment explanation
Indices: 27814--27938 Score: 146
Period size: 49 Copynumber: 2.5 Consensus size: 50
27804 AAATTTCTAG
* * * **
27814 ATTTTTCATCTCAGGGATACTCCAACCCCTGCTTTATTTCTAAAATATTG
1 ATTTTTCATCTCAGGGATACTCCAACCCCAGCTTTATTTCCAAAACATCA
* *
27864 ATTTTTCATCTC-GGGAATACTCTAA-CCCAGTTTTATTTCCAAAACATCA
1 ATTTTTCATCTCAGGG-ATACTCCAACCCCAGCTTTATTTCCAAAACATCA
*
27913 ATTTTTCATAATCAGGGATACTCCAA
1 ATTTTTCAT-CTCAGGGATACTCCAA
27939 TCCCGTTATT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
49 30 0.48
50 30 0.48
51 3 0.05
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.38
Consensus pattern (50 bp):
ATTTTTCATCTCAGGGATACTCCAACCCCAGCTTTATTTCCAAAACATCA
Found at i:28010 original size:79 final size:79
Alignment explanation
Indices: 27895--28253 Score: 359
Period size: 79 Copynumber: 4.5 Consensus size: 79
27885 CTAACCCAGT
* * * *
27895 TTTATTTCCAAAACATCAATTTTTCATAATCAGGGATACTCCAATCCCGTTATTTTTGAGGGGAT
1 TTTATTTCTAAAACATCGATTTTTCATAATCAGGGATACTCCAACCCCGTTATTTTCGAGGGGAT
*
27960 ACTCCAACCCCTGC
66 ACTCCAACCCCGGC
* * * * * * * *
27974 TTTATTTCTAAAATATTGATTTCTCATGATCGGGGATACTCCAACCCCGTTATTTTGGCGTGGAT
1 TTTATTTCTAAAACATCGATTTTTCATAATCAGGGATACTCCAACCCCGTTATTTTCGAGGGGAT
28039 ACTCCAACCCCGGC
66 ACTCCAACCCCGGC
* * * *
28053 CTTATTTCTAAAGCATCGATTTTTCACAATCCGGGATACTCCAACCCCGTTATTTTCGAGGGGAT
1 TTTATTTCTAAAACATCGATTTTTCATAATCAGGGATACTCCAACCCCGTTATTTTCGAGGGGAT
**
28118 ACTCCAACCCCGAT
66 ACTCCAACCCCGGC
* * * * * * *
28132 TTTATTT-TCAAA-GTGCCGA-TTTTCTATAATTAGGGATACTCTAACCCTGTTATTTTCAAAGG
1 TTTATTTCTAAAACAT--CGATTTTTC-ATAATCAGGGATACTCCAACCCCGTTATTTTCGAGGG
***
28194 GATACTCCAACCCCAAT
63 GATACTCCAACCCCGGC
* *
28211 TTTATTT-TCAAAACACCGATTTTCCATAATC-GAGGATACTCCA
1 TTTATTTCT-AAAACATCGATTTTTCATAATCAG-GGATACTCCA
28254 GCCCTATTGT
Statistics
Matches: 230, Mismatches: 43, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
77 1 0.00
78 9 0.04
79 213 0.93
80 7 0.03
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (79 bp):
TTTATTTCTAAAACATCGATTTTTCATAATCAGGGATACTCCAACCCCGTTATTTTCGAGGGGAT
ACTCCAACCCCGGC
Found at i:28216 original size:158 final size:158
Alignment explanation
Indices: 27880--28253 Score: 402
Period size: 158 Copynumber: 2.4 Consensus size: 158
27870 CATCTCGGGA
* * * * *
27880 ATACTCTAA-CCCAGTTTTATTTCCAAAACATCAATTTTTCATAATCAGGGATACTCCAATCCCG
1 ATACTCCAACCCCAGTTTTATTTCTAAAACATCGATTTTTCATAATCCGGGATACTCCAACCCCG
* ** * *
27944 TTATTTTTGAGGGGATACTCCAACCCCTGCTTTATTTCTAAAATATTGATTTCTCATGATCGGGG
66 TTATTTTCGAGGGGATACTCCAACCCCTGCTTTATTTCTAAAATACCGATTTCTCATAATCAGGG
***
28009 ATACTCCAACCCCGTTATTTTGGCGTGG
131 ATACTCCAACCCCGTTATTTTAAAGTGG
* ** * *
28037 ATACTCCAACCCCGGCCTTATTTCTAAAGCATCGATTTTTCACAATCCGGGATACTCCAACCCCG
1 ATACTCCAACCCCAGTTTTATTTCTAAAACATCGATTTTTCATAATCCGGGATACTCCAACCCCG
* * * *
28102 TTATTTTCGAGGGGATACTCCAACCCC-GATTTTATTT-TCAAAGTGCCGATTT-TCTATAATTA
66 TTATTTTCGAGGGGATACTCCAACCCCTG-CTTTATTTCT-AAAATACCGATTTCTC-ATAATCA
* *
28164 GGGATACTCTAACCCTGTTATTTTCAAAG-GG
128 GGGATACTCCAACCCCGTTATTTT-AAAGTGG
* * *
28195 ATACTCCAACCCCAATTTTATTT-TCAAAACACCGATTTTCCATAAT-CGAGGATACTCCA
1 ATACTCCAACCCCAGTTTTATTTCT-AAAACATCGATTTTTCATAATCCG-GGATACTCCA
28254 GCCCTATTGT
Statistics
Matches: 178, Mismatches: 32, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
157 15 0.08
158 162 0.91
159 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (158 bp):
ATACTCCAACCCCAGTTTTATTTCTAAAACATCGATTTTTCATAATCCGGGATACTCCAACCCCG
TTATTTTCGAGGGGATACTCCAACCCCTGCTTTATTTCTAAAATACCGATTTCTCATAATCAGGG
ATACTCCAACCCCGTTATTTTAAAGTGG
Found at i:34048 original size:20 final size:20
Alignment explanation
Indices: 34004--34061 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
33994 ATTTCAACGA
***
34004 TTTGTATCGATACATAAAGT
1 TTTGTATCGATACATATTTT
*
34024 GTTGTATCGATACATATTTT
1 TTTGTATCGATACATATTTT
34044 TTTGTATCGATACA-ATTT
1 TTTGTATCGATACATATTT
34062 AAGCTACTGC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (20 bp):
TTTGTATCGATACATATTTT
Found at i:34120 original size:13 final size:13
Alignment explanation
Indices: 34102--34126 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34092 ATTACTCAAA
34102 TGTATCGATACAT
1 TGTATCGATACAT
34115 TGTATCGATACA
1 TGTATCGATACA
34127 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:44231 original size:17 final size:16
Alignment explanation
Indices: 44198--44238 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
44188 GTAAAAAAAT
*
44198 AAAAAAAAACAACCAA
1 AAAAAAAAACAAACAA
44214 AAAAAAAAACAAAACAA
1 AAAAAAAAAC-AAACAA
44231 AGAAAAAA
1 A-AAAAAA
44239 GAGAGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.45
17 6 0.27
18 6 0.27
ACGTcount: A:0.85, C:0.12, G:0.02, T:0.00
Consensus pattern (16 bp):
AAAAAAAAACAAACAA
Found at i:44236 original size:21 final size:22
Alignment explanation
Indices: 44181--44238 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
44171 TCTTTTTTTT
44181 AAAA-AAAGTAAAAAAATAAAAA
1 AAAACAAAG-AAAAAAATAAAAA
** *
44203 AAAACAACCAAAAAAA-AAAAC
1 AAAACAAAGAAAAAAATAAAAA
44224 AAAACAAAGAAAAAA
1 AAAACAAAGAAAAAA
44239 GAGAGAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 17 0.57
22 11 0.37
23 2 0.07
ACGTcount: A:0.84, C:0.09, G:0.03, T:0.03
Consensus pattern (22 bp):
AAAACAAAGAAAAAAATAAAAA
Found at i:45387 original size:55 final size:54
Alignment explanation
Indices: 45320--45454 Score: 164
Period size: 55 Copynumber: 2.5 Consensus size: 54
45310 CTTTTTTCAC
* * *
45320 CCTTTAGTCTTCAAAGAGCGGGACATCATT-CAAAGCCCACATAAGCTGGTGGCA
1 CCTTTAGTCTTCAAAGAGCAGGAC-GCATTGCAAAGCCCACATAAGCAGGTGGCA
* * *
45374 CTTTTTAGTCTTCAAAGAGCAGGACGCCTTGCAAAGTCCACATAAGCAGGTGGCA
1 C-CTTTAGTCTTCAAAGAGCAGGACGCATTGCAAAGCCCACATAAGCAGGTGGCA
* * *
45429 CCTTCAGTCCTCAAAGAGCATGACGC
1 CCTTTAGTCTTCAAAGAGCAGGACGC
45455 CTTTTCCTTT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
54 25 0.36
55 44 0.64
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (54 bp):
CCTTTAGTCTTCAAAGAGCAGGACGCATTGCAAAGCCCACATAAGCAGGTGGCA
Found at i:46756 original size:61 final size:61
Alignment explanation
Indices: 45351--46780 Score: 1713
Period size: 61 Copynumber: 23.8 Consensus size: 61
45341 GACATCATTC
* * * * * *
45351 AAAGCCCACATAAGCTGGTGGCACTTTTTAGTCTTCAAAGAGCAGGACGCC--TTGC----
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
* * ** *
45406 AAAGTCCACATAAGCAGGTGGCACC-TTCAGTCCTCAAAGAGCATGACGCCTTTTCCTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
** *
45466 AAAGCCCACACAAGTTGGTGGCAATTTTCAGTCCTCAGAGAGCAGGACGCCTTTTCCTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
** * *
45527 AAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTTAAACAGCAGGACGCC-TTT-C----
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
* * *
45582 AAGGCCCACACAAGCTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGACGACTTTTCCTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
*
45642 AAAGCCCACACAAGTTGGTGGCACC-TTCTAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
* * * * * *
45703 AAAGCTCACACAAGTTGGTGGCACTTTTCAGTCCTCAAGGGGCAGGACACTTTTTCCTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
* * * *
45764 AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAGGGGCAGGACACCTTTTCCTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
* * ** *
45825 AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAGGAGCAGGACGCCTTCGCCTTTC
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
* * *
45886 AAAGCCCACACAAGCTAGTGGCACC-TTCAGTCCTCAAAGAGCGGGACGCCTTTTCCTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
* ** *
45946 AAAGCCCACACAAGTTGGTGGCATC-TTCTAGTCCTCAAAGAGTGGGACACCTTTTCCTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
* *
46007 AAAGGCCACACAAGTTGGTGGCACC-TTCTAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
* *
46068 AAAGCCCACATAAGTTGGT-GCACTTTTCCAGTCCTCAAAGAGCAGGACGCC-TTT-C----
1 AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
* *
46123 AAAGCCCACACAAGCTGGTGGCACC-TTCAGTCCTCAAAGAGCGGGACGCCTTTTCCTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
* * *
46183 AAAGCCCACACATGTTGATGGCACC-TTCTAGTCCTCAAAGAGCAGGACGCCTTCT-CTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
** * *
46243 CAAAGCCCACACAAGTTGGTGGCATTTTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTG
1 -AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
* * * *
46305 AAAGCCCACGCAAGTTGGCGGCACC-TTCTAGTCCTCAAAGAGCAGAACGTCTTTTCCTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
*
46366 AAAGCCCACACAAATTGGTGGCACC-TTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
* * * * *
46427 AAAGCCAACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACACATTTTCTTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
* * * * * *
46488 GAAGCCCACACAAGTTAGTGGCACTTTTCTAGTCCTCAAAGAGTAGGGCACCTTTTCCTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
* *
46550 AAAGCCCACAAAAGTTGGTGGCACC-TTCTAGTCCTCAAAGAGCAGGACGTCTTTTCCTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
** * *
46611 AAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTC-AAGAAGCAGGATGCCTTTTCCTATT
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG-AGCAGGACGCCTTTTCCTTTT
* * * * **
46672 AAAGCCCGCACAAGTTGGTGGCACCTTTCAGTCCTTAAAGAGCATGATG-CTTTCTCCTTGC
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTT-TCCTTTT
* * *
46733 AAAGCCCATACAAGTTGGTGGCACC-TTCTAGTCCCCAAAGAGTAGGAC
1 AAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGAC
46781 CTATTTCACT
Statistics
Matches: 1202, Mismatches: 136, Indels: 68
0.85 0.10 0.05
Matches are distributed among these distances:
54 66 0.05
55 68 0.06
56 9 0.01
59 2 0.00
60 152 0.13
61 837 0.70
62 68 0.06
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (61 bp):
AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
Found at i:47411 original size:20 final size:20
Alignment explanation
Indices: 47386--47509 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
47376 TTTTCACAAT
47386 TTGTATCGATACATGGTTTA
1 TTGTATCGATACATGGTTTA
47406 TTGTATCGATACATTCTGAGTTTTA
1 TTGTATCGATACA---TG-G-TTTA
* *
47431 TCTAGATGTATCGATACATTGTTCA
1 --T---TGTATCGATACATGGTTTA
* * *
47456 TTGTATCAATACATTGTTCA
1 TTGTATCGATACATGGTTTA
*
47476 TTGTATCGATACAT-TTTTCA
1 TTGTATCGATACATGGTTT-A
*
47496 ATGTATCGATACAT
1 TTGTATCGATACAT
47510 TCAGATATTT
Statistics
Matches: 86, Mismatches: 7, Indels: 22
0.75 0.06 0.19
Matches are distributed among these distances:
19 2 0.02
20 58 0.67
23 3 0.03
24 1 0.01
25 7 0.08
26 1 0.01
27 2 0.02
30 12 0.14
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (20 bp):
TTGTATCGATACATGGTTTA
Found at i:47510 original size:20 final size:20
Alignment explanation
Indices: 47436--47510 Score: 114
Period size: 20 Copynumber: 3.8 Consensus size: 20
47426 TTTTATCTAG
47436 ATGTATCGATACATTGTTCA
1 ATGTATCGATACATTGTTCA
* *
47456 TTGTATCAATACATTGTTCA
1 ATGTATCGATACATTGTTCA
* *
47476 TTGTATCGATACATTTTTCA
1 ATGTATCGATACATTGTTCA
47496 ATGTATCGATACATT
1 ATGTATCGATACATT
47511 CAGATATTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTGTTCA
Found at i:49858 original size:50 final size:50
Alignment explanation
Indices: 49795--49918 Score: 135
Period size: 50 Copynumber: 2.5 Consensus size: 50
49785 TAAATTTTTA
** * *
49795 GATTTTT-ATTCTCGGGGATACTCCGACCCCGGGTTTA-TTTCTAAAATATT
1 GATTTTTCA-TCTCGGGGATACTCAAACCCCGGGTTTATTTTC-AAAACATC
* *
49845 GATTTTTCATCTCGGGGATACTCAAACCTCGGTTTTATTTTCAAAACATC
1 GATTTTTCATCTCGGGGATACTCAAACCCCGGGTTTATTTTCAAAACATC
* *
49895 AATTTTTCATAATCGGGGATACTC
1 GATTTTTCAT-CTCGGGGATACTC
49919 TAATCCCATT
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
50 46 0.73
51 17 0.27
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (50 bp):
GATTTTTCATCTCGGGGATACTCAAACCCCGGGTTTATTTTCAAAACATC
Found at i:50030 original size:51 final size:51
Alignment explanation
Indices: 49937--50056 Score: 132
Period size: 51 Copynumber: 2.4 Consensus size: 51
49927 TTATTTTCGA
** * ** * **
49937 GGGGATACTCCAACCCCGATTTTATTTCTAAAATATTTATTTTTCATGATC
1 GGGGATACTCCAACCCCGACCTTATTTCTAAAACATCGATTTTCCACAATC
* * *
49988 GGGGATACTCCAACCCCGGCCTTATTTCTAAAGCATCGATTTTCCACAATT
1 GGGGATACTCCAACCCCGACCTTATTTCTAAAACATCGATTTTCCACAATC
*
50039 GGTGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
50057 TTATTTTCGA
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGACCTTATTTCTAAAACATCGATTTTCCACAATC
Found at i:50071 original size:79 final size:79
Alignment explanation
Indices: 49988--50207 Score: 189
Period size: 78 Copynumber: 2.8 Consensus size: 79
49978 TTTCATGATC
* *
49988 GGGGATACTCCAACCCCGGCCTTA-TTTCTAAAGCATCG-ATTTTCCACAATT-GGTGATACTCC
1 GGGGATACTCCAACCCCGACCTTATTTTC-AAAACAT-GAATTTTCCACAATTAGG-GATACTCC
50050 AACCCCGTTATTTTCGA
63 AACCCCGTTATTTTCGA
* ** * * * *
50067 GGGGATACT-CAACCTCGATTTTATTTTCAAAATATGAATTTTCTATAATTAGGGATACTCTAAC
1 GGGGATACTCCAACCCCGACCTTATTTTCAAAACATGAATTTTCCACAATTAGGGATACTCCAAC
*
50131 CCTGTTATTTTCGA
66 CCCGTTATTTTCGA
* * * ** * ** * *
50145 GGAGATACTCCAATCCTGATTTTATTTTCAGAACACCAATTTTCCATAA-TCGGAGATACTCCA
1 GGGGATACTCCAACCCCGACCTTATTTTCAAAACATGAATTTTCCACAATTAGG-GATACTCCA
50208 GCCCTGTTGT
Statistics
Matches: 115, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
77 1 0.01
78 60 0.52
79 54 0.47
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGACCTTATTTTCAAAACATGAATTTTCCACAATTAGGGATACTCCAAC
CCCGTTATTTTCGA
Found at i:50074 original size:130 final size:129
Alignment explanation
Indices: 49808--50132 Score: 370
Period size: 129 Copynumber: 2.5 Consensus size: 129
49798 TTTTATTCTC
* ** *
49808 GGGGATACTCCGACCCCGGGTTTATTTCTAAAATATTGATTTTTCATCTCGGGGATACTCAAACC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATATTGATTTTTCATATCGGGGATACTCAAACC
* ** * * * *
49873 TCGGTTTTATTTTCAAAACATCAATTTTTCATAATCGGGGATACTCTAATCCCATTATTTTCGA
66 CCGGCCTTATTTTCAAAACATCAATTTTCCACAATCGGGGATACTCCAACCCCATTATTTTCGA
* *
49937 GGGGATACTCCAACCCCGATTTTATTTCTAAAATATTTATTTTTCATGATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATATTGATTTTTCAT-ATCGGGGATACTCAAAC
* * * * *
50002 CCCGGCCTTA-TTTCTAAAGCATCGATTTTCCACAATTGGTGATACTCCAACCCCGTTATTTTCG
65 CCCGGCCTTATTTTC-AAAACATCAATTTTCCACAATCGGGGATACTCCAACCCCATTATTTTCG
50066 A
129 A
* * ** *
50067 GGGGATACT-CAACCTCGATTTTATTT-TCAAAATA-TGAATTTTCTATAATTAGGGATACTCTA
1 GGGGATACTCCAACCCCGATTTTATTTCT-AAAATATTGATTTTTC-AT-ATCGGGGATACTCAA
50129 ACCC
63 ACCC
50133 TGTTATTTTC
Statistics
Matches: 167, Mismatches: 25, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
128 8 0.05
129 87 0.52
130 72 0.43
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (129 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAATATTGATTTTTCATATCGGGGATACTCAAACC
CCGGCCTTATTTTCAAAACATCAATTTTCCACAATCGGGGATACTCCAACCCCATTATTTTCGA
Found at i:50091 original size:78 final size:79
Alignment explanation
Indices: 50026--50207 Score: 210
Period size: 78 Copynumber: 2.3 Consensus size: 79
50016 TAAAGCATCG
*
50026 ATTTTCCACAATT-GGTGATACTCCAACCCCGTTATTTTCGAGGGGATACT-CAA-CCTCGATTT
1 ATTTTCCACAATTAGG-GATACTCCAACCCCGTTATTTTCGAGGAGATACTCCAATCCT-GATTT
*
50088 TATTTTCAAAATATGA
64 TATTTTCAAAACATGA
* * * *
50104 ATTTTCTATAATTAGGGATACTCTAACCCTGTTATTTTCGAGGAGATACTCCAATCCTGATTTTA
1 ATTTTCCACAATTAGGGATACTCCAACCCCGTTATTTTCGAGGAGATACTCCAATCCTGATTTTA
* **
50169 TTTTCAGAACACCA
66 TTTTCAAAACATGA
* *
50183 ATTTTCCATAA-TCGGAGATACTCCA
1 ATTTTCCACAATTAGG-GATACTCCA
50208 GCCCTGTTGT
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
78 45 0.51
79 40 0.45
80 3 0.03
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.36
Consensus pattern (79 bp):
ATTTTCCACAATTAGGGATACTCCAACCCCGTTATTTTCGAGGAGATACTCCAATCCTGATTTTA
TTTTCAAAACATGA
Found at i:50213 original size:79 final size:77
Alignment explanation
Indices: 50026--50215 Score: 220
Period size: 79 Copynumber: 2.4 Consensus size: 77
50016 TAAAGCATCG
* * * *
50026 ATTTTCCACAATTGGTGATACTCCAACCCCGTTATTTTCGAGGGGATACTCAACCTCGATTTTAT
1 ATTTTCCATAATAGG-GATACTCCAACCCTGTTATTTTCGAGGAGATACTCAACCTCGATTTTAT
* **
50091 TTTCAAAATATGA
65 TTTCAAAACACCA
* *
50104 ATTTTCTATAATTAGGGATACTCTAACCCTGTTATTTTCGAGGAGATACTCCAATCCT-GATTTT
1 ATTTTCCATAA-TAGGGATACTCCAACCCTGTTATTTTCGAGGAGATACT-CAA-CCTCGATTTT
*
50168 ATTTTCAGAACACCA
63 ATTTTCAAAACACCA
* *
50183 ATTTTCCATAATCGGAGATACTCCAGCCCTGTT
1 ATTTTCCATAATAGG-GATACTCCAACCCTGTT
50216 GTTATCCCCA
Statistics
Matches: 94, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
78 43 0.46
79 48 0.51
80 3 0.03
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (77 bp):
ATTTTCCATAATAGGGATACTCCAACCCTGTTATTTTCGAGGAGATACTCAACCTCGATTTTATT
TTCAAAACACCA
Found at i:51172 original size:32 final size:33
Alignment explanation
Indices: 51131--51192 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
51121 CTTAACTGTT
* *
51131 TGTATCGATACA-CACAAGATGTATCGATAAAA
1 TGTATCGATACATCACAAAACGTATCGATAAAA
*
51163 TGTATCGATACATCCCAAAACGTATCGATA
1 TGTATCGATACATCACAAAACGTATCGATA
51193 CATTGGCTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 12 0.46
33 14 0.54
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (33 bp):
TGTATCGATACATCACAAAACGTATCGATAAAA
Found at i:57300 original size:19 final size:19
Alignment explanation
Indices: 57258--57329 Score: 74
Period size: 20 Copynumber: 3.7 Consensus size: 19
57248 ATATCCAGAA
*
57258 GTATCGATACAT-TATGCTTT
1 GTATCGATACATGT-T-CATT
57278 GTATCGATACATGTTCATT
1 GTATCGATACATGTTCATT
***
57297 GTATCGATACACACTCAATT
1 GTATCGATACATGTTC-ATT
57317 GTATCGATACATG
1 GTATCGATACATG
57330 AAACTGGAAG
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.36
20 27 0.61
21 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (19 bp):
GTATCGATACATGTTCATT
Found at i:61137 original size:9 final size:9
Alignment explanation
Indices: 61109--61138 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
61099 TCTGCGTCAA
61109 CTTCATCAT
1 CTTCATCAT
*
61118 CATCATCAT
1 CTTCATCAT
61127 CTTCATCAT
1 CTTCATCAT
61136 CTT
1 CTT
61139 TGACACTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.23, C:0.33, G:0.00, T:0.43
Consensus pattern (9 bp):
CTTCATCAT
Found at i:66576 original size:20 final size:20
Alignment explanation
Indices: 66551--66590 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
66541 AAGAATAACG
66551 CATGCTAGTCTTTGACCATT
1 CATGCTAGTCTTTGACCATT
*
66571 CATGCTAGTCTTTGAGCATT
1 CATGCTAGTCTTTGACCATT
66591 GCTAATAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (20 bp):
CATGCTAGTCTTTGACCATT
Found at i:68294 original size:58 final size:58
Alignment explanation
Indices: 68228--68599 Score: 301
Period size: 57 Copynumber: 6.5 Consensus size: 58
68218 GGATCATTTA
* * * * * *
68228 CAATTTCATACATTTTAGGGTCGTTTAAATAATTTTTCATGTTTTAAGGATTATTTTG
1 CAATTTCATGCATTTTAGGGTCATTTAAGTCATTTTTCATGATTTAAGGACTATTTTG
* * * * *
68286 CAATTTCATGCATTTTAGGTTTATTTAAGCCA-TTTTCATGATTTAAGAATTAATTTT-
1 CAATTTCATGCATTTTAGGGTCATTTAAGTCATTTTTCATGATTTAAGGACT-ATTTTG
* * * *
68343 TAATTTCATGCATTTTTGGTTCATTTAAGTCATTTTTCATGATTTAGGGACTATTTTG
1 CAATTTCATGCATTTTAGGGTCATTTAAGTCATTTTTCATGATTTAAGGACTATTTTG
* * ** * *
68401 CAATATT-AGGCATTTTAGGGTCATTTAATTCATTTCCCATGATTTAAGGACCATTTTT
1 CAAT-TTCATGCATTTTAGGGTCATTTAAGTCATTTTTCATGATTTAAGGACTATTTTG
* ** * * *
68459 CAATTTCAT-TATTTTATAGTCATTTAAGTCA-TTTTCTATGGTTT-AGAGACCATTTTA
1 CAATTTCATGCATTTTAGGGTCATTTAAGTCATTTTTC-ATGATTTAAG-GACTATTTTG
* *** * * * *
68516 CAATTTTATTTGTTTTAGGGTCATATAAGTCATTTTCCAGGATTT-AGGA-TCATTTTA
1 CAATTTCATGCATTTTAGGGTCATTTAAGTCATTTTTCATGATTTAAGGACT-ATTTTG
* * *
68573 CAATTTTATGCATTTTAAGATCATTTA
1 CAATTTCATGCATTTTAGGGTCATTTA
68600 TTTAGGACTA
Statistics
Matches: 254, Mismatches: 50, Indels: 21
0.78 0.15 0.06
Matches are distributed among these distances:
56 5 0.02
57 122 0.48
58 121 0.48
59 6 0.02
ACGTcount: A:0.27, C:0.11, G:0.13, T:0.48
Consensus pattern (58 bp):
CAATTTCATGCATTTTAGGGTCATTTAAGTCATTTTTCATGATTTAAGGACTATTTTG
Found at i:68435 original size:115 final size:112
Alignment explanation
Indices: 68228--68588 Score: 305
Period size: 115 Copynumber: 3.1 Consensus size: 112
68218 GGATCATTTA
* * * * * * *
68228 CAATTTCATACATTTTAGGGTCGTTTAAATAATTTTTCATGTTTTAAGGATTATTTTGCAATTTC
1 CAATTTCAT-CATTTT-TGGTCATTTAAGTCATTTTTCATGATTTAGGGACTATTTTGCAATTT-
* * * *
68293 ATGCATTTTAGGTTTATTTAAGCCATTTTCATGATTTAAGAATTAATTTTT
63 ATGCATTTTAGGGTCATTTAAGTCATTTTCATGATTTAAGAA-CAATTTTT
68344 -AATTTCATGCATTTTTGGTTCATTTAAGTCATTTTTCATGATTTAGGGACTATTTTGCAATATT
1 CAATTTCAT-CATTTTTGG-TCATTTAAGTCATTTTTCATGATTTAGGGACTATTTTGCAAT-TT
* * * * *
68408 AGGCATTTTAGGGTCATTTAATTCATTTCCCATGATTTAAGGACCATTTTT
63 ATGCATTTTAGGGTCATTTAAGTCATTT-TCATGATTTAAGAACAATTTTT
* * * * * *
68459 CAATTTCATTATTTTATAGTCATTTAAGTCA-TTTTCTATGGTTTAGAGACCATTTTACAATTTT
1 CAATTTCATCATTTT-TGGTCATTTAAGTCATTTTTC-ATGATTTAGGGACTATTTTGCAA-TTT
*** * * * * *
68523 ATTTGTTTTAGGGTCATATAAGTCATTTTCCAGGATTTAGGATC-ATTTTA
63 ATGCATTTTAGGGTCATTTAAGTCATTTT-CATGATTTAAGAACAATTTTT
*
68573 CAATTTTATGCATTTT
1 CAATTTCAT-CATTTT
68589 AAGATCATTT
Statistics
Matches: 199, Mismatches: 37, Indels: 19
0.78 0.15 0.07
Matches are distributed among these distances:
114 20 0.10
115 154 0.77
116 25 0.13
ACGTcount: A:0.27, C:0.11, G:0.13, T:0.49
Consensus pattern (112 bp):
CAATTTCATCATTTTTGGTCATTTAAGTCATTTTTCATGATTTAGGGACTATTTTGCAATTTATG
CATTTTAGGGTCATTTAAGTCATTTTCATGATTTAAGAACAATTTTT
Found at i:70693 original size:58 final size:58
Alignment explanation
Indices: 70630--70748 Score: 193
Period size: 58 Copynumber: 2.1 Consensus size: 58
70620 CATATCCAAA
* * *
70630 GTATTACGCAAAGATATTACTATATATAGTGACCTTAAAAAATGTCTTTATGACACTT
1 GTATTACACAAAGAGATTACTATATATAGTGACCTTAAAAAATGTCCTTATGACACTT
* *
70688 GTATTATACAAAGAGATTACTATATATAGTGACCTTAAAAAATGTCCTTATGACGCTT
1 GTATTACACAAAGAGATTACTATATATAGTGACCTTAAAAAATGTCCTTATGACACTT
70746 GTA
1 GTA
70749 AGCAAAATCT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35
Consensus pattern (58 bp):
GTATTACACAAAGAGATTACTATATATAGTGACCTTAAAAAATGTCCTTATGACACTT
Found at i:72575 original size:21 final size:21
Alignment explanation
Indices: 72524--72578 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
72514 GAGGGCCCGG
* *
72524 GCTCCGCCACAGCCATCATCA
1 GCTCCTCCACCGCCATCATCA
72545 GCTCCTCCACCGCCATCATCA
1 GCTCCTCCACCGCCATCATCA
72566 GCT-CTCCCACCGC
1 GCTCCT-CCACCGC
72579 TTCCCATGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 2 0.06
21 29 0.94
ACGTcount: A:0.18, C:0.53, G:0.13, T:0.16
Consensus pattern (21 bp):
GCTCCTCCACCGCCATCATCA
Found at i:74501 original size:2 final size:2
Alignment explanation
Indices: 74494--74524 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
74484 GCGTTATTGG
74494 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
74525 GTGGTAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:75474 original size:72 final size:71
Alignment explanation
Indices: 75320--75474 Score: 179
Period size: 72 Copynumber: 2.2 Consensus size: 71
75310 TTAAAATATT
* * * * *
75320 TTTATTAACAATAGGATTTATCACATTGATAAATAAAAATTCTAAATATATTAAAAATTTGGTTC
1 TTTATTAATAATAGAATTTATCACATTGATAAATAAAAATTCTAAATATATGAAAAATTTGGGTA
*
75385 AATTAA
66 AATAAA
* * *
75391 TTTATTGAATAATAGAATTTATCACATT-ATAAATAAAAATTTTAATTTTACTGAAAAATTATGG
1 TTTATT-AATAATAGAATTTATCACATTGATAAATAAAAATTCTAAATATA-TGAAAAATT-TGG
75455 GTAAATGAAA
63 GTAAAT-AAA
75465 TTTA-TAATAA
1 TTTATTAATAA
75475 ATAAAAAAAT
Statistics
Matches: 71, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
71 25 0.35
72 32 0.45
73 8 0.11
74 6 0.08
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (71 bp):
TTTATTAATAATAGAATTTATCACATTGATAAATAAAAATTCTAAATATATGAAAAATTTGGGTA
AATAAA
Found at i:79870 original size:13 final size:13
Alignment explanation
Indices: 79852--79877 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
79842 TACACCAAGT
79852 ATGTATCGATACA
1 ATGTATCGATACA
79865 ATGTATCGATACA
1 ATGTATCGATACA
79878 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:79875 original size:32 final size:33
Alignment explanation
Indices: 79834--79897 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
79824 TAGCCAAACT
* **
79834 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
79866 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
79898 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:82126 original size:22 final size:22
Alignment explanation
Indices: 82099--82154 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
82089 TTGCAAGTTG
82099 AAATAAAGAACTTGGCTAATG-A
1 AAATAAAGAACTTGGCTAA-GAA
* *
82121 AAATAATGAA-TTAGCTAAGAA
1 AAATAAAGAACTTGGCTAAGAA
82142 AAATAAA-AACTTG
1 AAATAAAGAACTTG
82155 CATGATTCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 3 0.11
21 16 0.57
22 9 0.32
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.23
Consensus pattern (22 bp):
AAATAAAGAACTTGGCTAAGAA
Done.