Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1910
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: 16896
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:842 original size:42 final size:42
Alignment explanation
Indices: 735--1229 Score: 254
Period size: 42 Copynumber: 11.8 Consensus size: 42
725 TTCATTTTCT
* * *
735 TATCCCTCAGTCTGCCTGTTGACTTTGACCTTGGAGACTGTCC
1 TATCACTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACT-TCC
* * *
778 TAT--CTCAGTTTGCTTGTTGGCTTTGACCTTGGAGACTTCC
1 TATCACTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTCC
* *
818 TATCACTCAGTCTGCTTGTCGGCTTTGACCTTGGAGACTACC
1 TATCACTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTCC
* * *
860 T-T-ATCTCAGTCTACCTATCGGC-TTGACCTTGGAGACTTTC
1 TATCA-CTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTCC
* * *
900 -ATTACCCTCAGTCTGCCTGTCGGCTTTGATCC-TAGAGACTACCC
1 TA-T-CACTCAGTCTGCCTGTCGGCTTTGA-CCTTGGAGACT-TCC
* * * * * *
944 TAT--TTAAGTCTACCTGTTGGCTTTGACCCTGAAGA-TTGCC
1 TATCACTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTT-CC
* * * * *
984 --TCATCTAAAGTTTGCCTGTCAGCTTTGACCCTGAAGACTTTCC
1 TATCA-CT-CAGTCTGCCTGTCGGCTTTGACCTTGGAGAC-TTCC
* * * * * *
1027 TA-CCCTTAGTCTGCCTATCGGCTTTGACCCTGGAAACTGCC
1 TATCACTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTCC
* ** * *
1068 T-T-ATCTAAAGTCTAACTGTCGGCTTTGACCTTGAAGACTT-T
1 TATCA-CT-CAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTCC
* * * * * *
1109 TTTCCCCCTTAGTCTGCTTGTCGGCTTTGATCTTGGAGACTGCC
1 TAT--CACTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTCC
* * * *
1153 --TCATCTAAAGTTTACCTGTCGGCTTTGACCTTGGAGACTTTC
1 TATCA-CT-CAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTCC
* * * *
1195 T-TACCCTCAATTTGCCTGTTGGCTTTGACCTTGGA
1 TAT-CACTCAGTCTGCCTGTCGGCTTTGACCTTGGA
1230 CACTACTTTA
Statistics
Matches: 350, Mismatches: 69, Indels: 67
0.72 0.14 0.14
Matches are distributed among these distances:
38 1 0.00
40 29 0.08
41 81 0.23
42 181 0.52
43 47 0.13
44 10 0.03
45 1 0.00
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.36
Consensus pattern (42 bp):
TATCACTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTCC
Found at i:883 original size:83 final size:82
Alignment explanation
Indices: 735--971 Score: 273
Period size: 83 Copynumber: 2.9 Consensus size: 82
725 TTCATTTTCT
* * * * * *
735 TATCCCTCAGTCTGCCTGTTGACTTTGACCTTGGAGACTGTCCTATCTCAGTTTGCTTGTTGGCT
1 TATCCCTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACT-ACCTATCTCAGTCTACCTGTTGGCT
800 TTGACCTTGGAGACTTCC
65 TTGACCTTGGAGACTTCC
* * * *
818 TATCACTCAGTCTGCTTGTCGGCTTTGACCTTGGAGACTACCTTATCTCAGTCTACCTATCGGC-
1 TATCCCTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTACC-TATCTCAGTCTACCTGTTGGCT
*
882 TTGACCTTGGAGACTTTC
65 TTGACCTTGGAGACTTCC
* * *
900 -ATTACCCTCAGTCTGCCTGTCGGCTTTGATCC-TAGAGACTACCCTATTTAAGTCTACCTGTTG
1 TA-T-CCCTCAGTCTGCCTGTCGGCTTTGA-CCTTGGAGACTA-CCTATCTCAGTCTACCTGTTG
963 GCTTTGACC
62 GCTTTGACC
972 CTGAAGATTG
Statistics
Matches: 130, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
81 1 0.01
82 20 0.15
83 99 0.76
84 10 0.08
ACGTcount: A:0.16, C:0.28, G:0.20, T:0.36
Consensus pattern (82 bp):
TATCCCTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTACCTATCTCAGTCTACCTGTTGGCTT
TGACCTTGGAGACTTCC
Found at i:1164 original size:169 final size:169
Alignment explanation
Indices: 962--1274 Score: 419
Period size: 169 Copynumber: 1.9 Consensus size: 169
952 TCTACCTGTT
* *
962 GGCTTTGACCCTGAAGATTGCCTCATCTAAAGTTTGCCTGTCAGCTTTGACCCTGAAGACTTTCC
1 GGCTTTGACCCTGAAGACTGCCTCATCTAAAGTTTACCTGTCAGCTTTGACCCTGAAGACTTTCC
* * * *
1027 TACCCTTAGTCTGCCTATCGGCTTTGACCCTGGAAACTGCCTTATCTAAAGTCTAACTGTCGGCT
66 TACCCTCAATCTGCCTATCGGCTTTGACCCTGGAAACTACCTTATCTAAAGTCTAACTGTCGACT
1092 TTGACCTTGAAGACTTTTTTCCCCCTTAGTCTGCTTGTC
131 TTGACCTTGAAGACTTTTTTCCCCCTTAGTCTGCTTGTC
* * * * * * *
1131 GGCTTTGATCTTGGAGACTGCCTCATCTAAAGTTTACCTGTCGGCTTTGACCTTGGAGACTTTCT
1 GGCTTTGACCCTGAAGACTGCCTCATCTAAAGTTTACCTGTCAGCTTTGACCCTGAAGACTTTCC
* * * * * * * **
1196 TACCCTCAATTTGCCTGTTGGCTTTGACCTTGGACACTACTTTATTTAAAGTCTGTCTGTCGACT
66 TACCCTCAATCTGCCTATCGGCTTTGACCCTGGAAACTACCTTATCTAAAGTCTAACTGTCGACT
*
1261 TTGACCTTGGAGAC
131 TTGACCTTGAAGAC
1275 CGCCTTATTT
Statistics
Matches: 121, Mismatches: 23, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
169 121 1.00
ACGTcount: A:0.18, C:0.26, G:0.19, T:0.36
Consensus pattern (169 bp):
GGCTTTGACCCTGAAGACTGCCTCATCTAAAGTTTACCTGTCAGCTTTGACCCTGAAGACTTTCC
TACCCTCAATCTGCCTATCGGCTTTGACCCTGGAAACTACCTTATCTAAAGTCTAACTGTCGACT
TTGACCTTGAAGACTTTTTTCCCCCTTAGTCTGCTTGTC
Found at i:1256 original size:84 final size:84
Alignment explanation
Indices: 950--1274 Score: 328
Period size: 84 Copynumber: 3.9 Consensus size: 84
940 ACCCTATTTA
* * * * * * * *
950 AGTCTACCTGTTGGCTTTGACCCT-GAAGATTGCCTCATCTAAAGTTTGCCTGTCAGCTTTGACC
1 AGTCTGCCTGTCGGCTTTGACCTTGGAA-ACTGCCTTATCTAAAGTCTACCTGTCGGCTTTGACC
* *
1014 CTGAAGACTTTCCTACCCTT
65 TTGAAGACTTTCTTACCCTT
* * *
1034 AGTCTGCCTATCGGCTTTGACCCTGGAAACTGCCTTATCTAAAGTCTAACTGTCGGCTTTGACCT
1 AGTCTGCCTGTCGGCTTTGACCTTGGAAACTGCCTTATCTAAAGTCTACCTGTCGGCTTTGACCT
* *
1099 TGAAGACTTTTTTCCCCCTT
66 TGAAGACTTTCTT-ACCCTT
* * * * *
1119 AGTCTGCTTGTCGGCTTTGATCTTGGAGACTGCCTCATCTAAAGTTTACCTGTCGGCTTTGACCT
1 AGTCTGCCTGTCGGCTTTGACCTTGGAAACTGCCTTATCTAAAGTCTACCTGTCGGCTTTGACCT
* *
1184 TGGAGACTTTCTTACCCTC
66 TGAAGACTTTCTTACCCTT
* * * * * * * ** *
1203 AATTTGCCTGTTGGCTTTGACCTTGGACACTACTTTATTTAAAGTCTGTCTGTCGACTTTGACCT
1 AGTCTGCCTGTCGGCTTTGACCTTGGAAACTGCCTTATCTAAAGTCTACCTGTCGGCTTTGACCT
*
1268 TGGAGAC
66 TGAAGAC
1275 CGCCTTATTT
Statistics
Matches: 200, Mismatches: 39, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
84 124 0.62
85 76 0.38
ACGTcount: A:0.18, C:0.26, G:0.19, T:0.36
Consensus pattern (84 bp):
AGTCTGCCTGTCGGCTTTGACCTTGGAAACTGCCTTATCTAAAGTCTACCTGTCGGCTTTGACCT
TGAAGACTTTCTTACCCTT
Found at i:1263 original size:42 final size:42
Alignment explanation
Indices: 1207--1307 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 42
1197 ACCCTCAATT
* * * *
1207 TGCCTGTTGGCTTTGACCTTGGACACTACTTTATTTAAAGTC
1 TGCCTGTCGACTTTGACCTTGGACACCACCTTATTTAAAGTC
* * * *
1249 TGTCTGTCGACTTTGACCTTGGAGACCGCCTTATTTAAAGTT
1 TGCCTGTCGACTTTGACCTTGGACACCACCTTATTTAAAGTC
*
1291 TGCCTGTCGGCTTTGAC
1 TGCCTGTCGACTTTGAC
1308 TCGAGAGAAT
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.17, C:0.23, G:0.22, T:0.39
Consensus pattern (42 bp):
TGCCTGTCGACTTTGACCTTGGACACCACCTTATTTAAAGTC
Found at i:1868 original size:31 final size:31
Alignment explanation
Indices: 1791--1895 Score: 130
Period size: 31 Copynumber: 3.4 Consensus size: 31
1781 ATATAATAAT
*
1791 AAAATAATAAAAAA--AATT-AAAATTCACAA
1 AAAATAAAAAAAAATCAATTAAAAATTCA-AA
1820 AAAA-AAAATTAATAAATCAATTAAAAATTCAAA
1 AAAATAAAA--AA-AAATCAATTAAAAATTCAAA
1853 AAAATAAAAAAAAATCAATTAAAAATTC-AA
1 AAAATAAAAAAAAATCAATTAAAAATTCAAA
1883 AAAATAAAAAAAA
1 AAAATAAAAAAAA
1896 CCAAAAAAAC
Statistics
Matches: 68, Mismatches: 1, Indels: 13
0.83 0.01 0.16
Matches are distributed among these distances:
28 3 0.04
29 4 0.06
30 17 0.25
31 20 0.29
32 2 0.03
33 10 0.15
34 12 0.18
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.20
Consensus pattern (31 bp):
AAAATAAAAAAAAATCAATTAAAAATTCAAA
Found at i:1884 original size:21 final size:21
Alignment explanation
Indices: 1805--1886 Score: 55
Period size: 21 Copynumber: 3.9 Consensus size: 21
1795 TAATAAAAAA
**
1805 AATT-AAAATTCACAAAAAAAA
1 AATTAAAAATTCA-AAAAAATC
1826 AATTAATAAA-TCAATTAAAAATTC
1 AATTAA-AAATTCAA--AAAAA-TC
**
1850 AA--AAAAATAAAAAAAAATC
1 AATTAAAAATTCAAAAAAATC
1869 AATTAAAAATTCAAAAAA
1 AATTAAAAATTCAAAAAA
1887 TAAAAAAAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 16
0.68 0.09 0.23
Matches are distributed among these distances:
19 4 0.09
20 5 0.11
21 20 0.43
22 8 0.17
23 8 0.17
24 2 0.04
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.22
Consensus pattern (21 bp):
AATTAAAAATTCAAAAAAATC
Found at i:1885 original size:39 final size:38
Alignment explanation
Indices: 1819--1904 Score: 93
Period size: 39 Copynumber: 2.2 Consensus size: 38
1809 AAAATTCACA
* * * *
1819 AAAAAAAAATTAATAAATCAATTAAAAATTCAAAAAAAT
1 AAAAAAAAATCAATAAA-CAATTAAAAAATAAAAAAAAC
1858 AAAAAAAAATCAATTAAA-AATTCAAAAAATAAAAAAAAC
1 AAAAAAAAATCAA-TAAACAATT-AAAAAATAAAAAAAAC
*
1897 CAAAAAAA
1 AAAAAAAA
1905 CAAAAAAACA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
38 4 0.10
39 32 0.80
40 4 0.10
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (38 bp):
AAAAAAAAATCAATAAACAATTAAAAAATAAAAAAAAC
Found at i:1900 original size:17 final size:18
Alignment explanation
Indices: 1880--1927 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
1870 ATTAAAAATT
1880 CAAAAAATA-AAAAAAAC
1 CAAAAAATACAAAAAAAC
1897 CAAAAAA-ACAAAAAAAC
1 CAAAAAATACAAAAAAAC
*
1914 AAAAAAATCACAAA
1 CAAAAAAT-ACAAA
1928 TTAAAGAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 1 0.04
17 21 0.78
19 5 0.19
ACGTcount: A:0.81, C:0.15, G:0.00, T:0.04
Consensus pattern (18 bp):
CAAAAAATACAAAAAAAC
Found at i:1918 original size:9 final size:9
Alignment explanation
Indices: 1881--1920 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
1871 TTAAAAATTC
*
1881 AAAAAATAA
1 AAAAAACAA
*
1890 AAAAAACCA
1 AAAAAACAA
1899 AAAAAAC-A
1 AAAAAACAA
1907 AAAAAACAA
1 AAAAAACAA
1916 AAAAA
1 AAAAA
1921 TCACAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 8 0.29
9 20 0.71
ACGTcount: A:0.88, C:0.10, G:0.00, T:0.03
Consensus pattern (9 bp):
AAAAAACAA
Found at i:2776 original size:19 final size:21
Alignment explanation
Indices: 2728--2782 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
2718 AATTTCAATA
*
2728 ATTTGTATCGATACATTCAGT
1 ATTTGTATCGATACATTAAGT
**
2749 AAATGTATCGATACA-TAAGT
1 ATTTGTATCGATACATTAAGT
2769 -TTTGTATCGATACA
1 ATTTGTATCGATACA
2783 ATGTATCGCT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 12 0.41
20 4 0.14
21 13 0.45
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (21 bp):
ATTTGTATCGATACATTAAGT
Found at i:2833 original size:21 final size:21
Alignment explanation
Indices: 2807--2848 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2797 GGCTACTGCC
* *
2807 AAGGAAATGTATCGATTCATT
1 AAGGAAATGTATAGATACATT
*
2828 AAGGAAGTGTATAGATACATT
1 AAGGAAATGTATAGATACATT
2849 GTATCGATAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.31
Consensus pattern (21 bp):
AAGGAAATGTATAGATACATT
Found at i:5381 original size:79 final size:78
Alignment explanation
Indices: 5261--5453 Score: 211
Period size: 79 Copynumber: 2.5 Consensus size: 78
5251 TTCCATTTCC
*
5261 AAAA-CATCAATTTTT--C-ATCGGGGATACTCCTATCCCGTTATTTCCGAAGGGATACTCCAA-
1 AAAATCATCAATTTTTCACAATCGGGGATACTCC-AACCCGTTATTTCCGAAGGGATACTCCAAT
*
5321 CCTCGGTTTTATTTAT
65 CC-CGATTTTATTT-T
* * * *
5337 AAAAT-ATTAATTTCTT-ATAATCGGGGATACTCCAACCTCGTTATTTTCGAGGGGATACTCCAA
1 AAAATCATCAATTT-TTCACAATCGGGGATACTCCAACC-CGTTATTTCCGAAGGGATACTCCAA
5400 TCCCGATTTTATTTT
64 TCCCGATTTTATTTT
* * *
5415 TAAATCATCGATTTTTCACAATCGGGGATACTCGAACCC
1 AAAATCATCAATTTTTCACAATCGGGGATACTCCAACCC
5454 TAGTTTTATT
Statistics
Matches: 98, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
76 11 0.11
77 2 0.02
78 11 0.11
79 72 0.73
80 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (78 bp):
AAAATCATCAATTTTTCACAATCGGGGATACTCCAACCCGTTATTTCCGAAGGGATACTCCAATC
CCGATTTTATTTT
Found at i:5461 original size:51 final size:50
Alignment explanation
Indices: 5387--5504 Score: 139
Period size: 51 Copynumber: 2.3 Consensus size: 50
5377 TTATTTTCGA
* * *
5387 GGGGATACTCCAATCCCGATTTTATTT-TTAAATCATCGATTTTTCACAATC
1 GGGGATACTCCAA-CCCGATTTTATTTCTAAAAT-ATCAATTTCTCACAATC
* * * *
5438 GGGGATACTCGAACCCTAGTTTTATTTCTAAAATATTAATTTCTCATAATC
1 GGGGATACTCCAACCCGA-TTTTATTTCTAAAATATCAATTTCTCACAATC
5489 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
5505 CATTATTTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
50 4 0.07
51 48 0.84
52 5 0.09
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.36
Consensus pattern (50 bp):
GGGGATACTCCAACCCGATTTTATTTCTAAAATATCAATTTCTCACAATC
Found at i:5475 original size:130 final size:131
Alignment explanation
Indices: 5309--5583 Score: 437
Period size: 130 Copynumber: 2.1 Consensus size: 131
5299 TATTTCCGAA
* *
5309 GGGATACTCCAA-CCTCGGTTTTATTTATAAAATATTAATTTCTTATAATCGGGGATACTCCAAC
1 GGGATACTCCAACCCTCAGTTTTATTTATAAAATATTAATTTCTCATAATCGGGGATACTCCAAC
* * * *
5373 CTCGTTATTTTCGAGGGGATACTCCAATCCCGATTTTATTTTTAAATCATCGATTTTTCACAATC
66 CCCATTATTTTCGAAGGGATACTCCAATCCCGATTTTATTTCTAAATCATCGATTTTTCACAATC
5438 G
131 G
* *
5439 GGGATACTCGAACCCT-AGTTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATACTCCAAC
1 GGGATACTCCAACCCTCAGTTTTATTTATAAAATATTAATTTCTCATAATCGGGGATACTCCAAC
* *
5503 CCCATTATTTTTGAAGGGATACTCCAATCCCGATTTTATTTCTAAATCATCGATTTTTCATAATC
66 CCCATTATTTTCGAAGGGATACTCCAATCCCGATTTTATTTCTAAATCATCGATTTTTCACAATC
5568 G
131 G
*
5569 GAGATACTCCAACCC
1 GGGATACTCCAACCC
5584 CGTTATTTTC
Statistics
Matches: 132, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
130 129 0.98
131 3 0.02
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (131 bp):
GGGATACTCCAACCCTCAGTTTTATTTATAAAATATTAATTTCTCATAATCGGGGATACTCCAAC
CCCATTATTTTCGAAGGGATACTCCAATCCCGATTTTATTTCTAAATCATCGATTTTTCACAATC
G
Found at i:5522 original size:79 final size:77
Alignment explanation
Indices: 5439--5643 Score: 243
Period size: 79 Copynumber: 2.6 Consensus size: 77
5429 TTCACAATCG
* * *
5439 GGGATACTCGAACCCTAGTTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATACTCCAACC
1 GGGATACTCCAACCC-AGTTTTATTTCTAAAATATTAATTTTTCATAATCGGAGATACTCCAACC
*
5504 CCATTATTTTTGAA
65 CCATTATTTTCG-A
**
5518 GGGATACTCCAATCCC-GATTTTATTTCT-AAATCATCGATTTTTCATAATCGGAGATACTCCAA
1 GGGATACTCCAA-CCCAG-TTTTATTTCTAAAAT-ATTAATTTTTCATAATCGGAGATACTCCAA
*
5581 CCCCGTTATTTTCGA
63 CCCCATTATTTTCGA
* *
5596 GGAGATACTCCAACCCCGTTGTTATCTCTAAAATATTAAATTTTTCAT
1 GG-GATACTCCAACCCAGTT-TTATTTCTAAAATATT-AATTTTTCAT
5644 CGAGAGAGGT
Statistics
Matches: 108, Mismatches: 10, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
78 13 0.12
79 79 0.73
80 16 0.15
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (77 bp):
GGGATACTCCAACCCAGTTTTATTTCTAAAATATTAATTTTTCATAATCGGAGATACTCCAACCC
CATTATTTTCGA
Found at i:6932 original size:71 final size:72
Alignment explanation
Indices: 6782--6944 Score: 204
Period size: 71 Copynumber: 2.3 Consensus size: 72
6772 CCAACCCACG
* * * * * *
6782 AGCACCCAAAACCAGTAGCTCTAGCAGCTTCCACGAACATTAGTAACAGCTCCAGCAGCTTCTAG
1 AGCACCCGAAACCAGCAGCTCCAACAGCTTCCACGAACATTAGTAACAGCTCCAACAACTTCTAG
*
6847 TAGCGAT
66 TAGCGAC
* * *
6854 AGCACCCGAAACCAGCAGGTCCAACAGCTTCCACGAACA-TCG-ACGCAGCTCCAACAACTTCTA
1 AGCACCCGAAACCAGCAGCTCCAACAGCTTCCACGAACATTAGTA-ACAGCTCCAACAACTTCTA
6917 GTAGCGAC
65 GTAGCGAC
*
6925 AGCACCCGAAACTAGCAGCT
1 AGCACCCGAAACCAGCAGCT
6945 TCCATGAACA
Statistics
Matches: 78, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
70 1 0.01
71 43 0.55
72 34 0.44
ACGTcount: A:0.33, C:0.34, G:0.18, T:0.15
Consensus pattern (72 bp):
AGCACCCGAAACCAGCAGCTCCAACAGCTTCCACGAACATTAGTAACAGCTCCAACAACTTCTAG
TAGCGAC
Found at i:7079 original size:64 final size:65
Alignment explanation
Indices: 6985--7108 Score: 160
Period size: 64 Copynumber: 1.9 Consensus size: 65
6975 GACAACATCC
**
6985 AACAACAGCAGCAACTTCCAGCCCACGAGCACTCTAGTAGCTACCAGCA-GCAACAGCATCCACG
1 AACAACAGCAGCAACTTCCAGCCCACGAGCACTCTAACAGCTACCAGCACGCAACAGCATCCACG
* * * * * *
7049 AACATCAGTAGCAGCTTCCAGCCCATGAGCACTTTAACAGCTTCCAGCACGGCAACAGCA
1 AACAACAGCAGCAACTTCCAGCCCACGAGCACTCTAACAGCTACCAGCAC-GCAACAGCA
7109 ACAGCAACTC
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
64 41 0.82
66 9 0.18
ACGTcount: A:0.33, C:0.35, G:0.18, T:0.14
Consensus pattern (65 bp):
AACAACAGCAGCAACTTCCAGCCCACGAGCACTCTAACAGCTACCAGCACGCAACAGCATCCACG
Found at i:8886 original size:69 final size:70
Alignment explanation
Indices: 8791--8931 Score: 239
Period size: 69 Copynumber: 2.0 Consensus size: 70
8781 AAAGACATTT
*
8791 TGACCTTGAAAAACCTTTTATATTCCTCTGAGCTTCTAGCAAGATATAAAAGAGAATAATAAAAT
1 TGACCTTGAAAAACCTTTTATATTCCTCCGAGCTTCTAGCAAGATATAAAAGAGAATAATAAAAT
8856 TCACG
66 TCACG
* * *
8861 TGACCTTG-AAAACCTTTTATATTCCTCCGGGCTTCTAGCAGGATATAAAAGAGAATAATAAAGT
1 TGACCTTGAAAAACCTTTTATATTCCTCCGAGCTTCTAGCAAGATATAAAAGAGAATAATAAAAT
8925 TCACG
66 TCACG
8930 TG
1 TG
8932 TTCCACGAGA
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
69 59 0.88
70 8 0.12
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.30
Consensus pattern (70 bp):
TGACCTTGAAAAACCTTTTATATTCCTCCGAGCTTCTAGCAAGATATAAAAGAGAATAATAAAAT
TCACG
Found at i:10505 original size:31 final size:31
Alignment explanation
Indices: 10467--10535 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
10457 TTTAAAACTC
*
10467 AAGCTCAATTTAAGATAATATCAAATTATTT
1 AAGCTCAATTTAAGATAAAATCAAATTATTT
*
10498 AAGCTCAATTTAAGATAAAATTAAATTATTT
1 AAGCTCAATTTAAGATAAAATCAAATTATTT
*
10529 AAACTCA
1 AAGCTCA
10536 CTCGATTAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.36
Consensus pattern (31 bp):
AAGCTCAATTTAAGATAAAATCAAATTATTT
Found at i:11056 original size:34 final size:33
Alignment explanation
Indices: 11017--11114 Score: 90
Period size: 34 Copynumber: 2.9 Consensus size: 33
11007 TGTTATATAA
*
11017 ATTATTTTTAAATTTATTATACTGTATTTATTAT
1 ATTATTTTTAAATTTATTATA-TATATTTATTAT
* * * *
11051 ATTATTATGATATTTATTATATTTTATATT-TTAT
1 ATTATTTTTAAATTTATTATA-TATAT-TTATTAT
* * *
11085 ATCATATTTAAAATTATTATATATATTTAT
1 ATTATTTTTAAATTTATTATATATATTTAT
11115 ACCCTCCTAT
Statistics
Matches: 50, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
32 2 0.04
33 5 0.10
34 41 0.82
35 2 0.04
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (33 bp):
ATTATTTTTAAATTTATTATATATATTTATTAT
Found at i:11091 original size:19 final size:19
Alignment explanation
Indices: 11064--11113 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
11054 ATTATGATAT
* *
11064 TTAT-TATATTTTATATT-
1 TTATATATATTTAAAATTA
11081 TTATATCATATTTAAAATTA
1 TTATAT-ATATTTAAAATTA
11101 TTATATATATTTA
1 TTATATATATTTA
11114 TACCCTCCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 4 0.14
18 1 0.04
19 17 0.61
20 6 0.21
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TTATATATATTTAAAATTA
Found at i:11553 original size:14 final size:16
Alignment explanation
Indices: 11534--11565 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
11524 ACATATTTTT
11534 TAATATT-TATAT-TA
1 TAATATTATATATATA
11548 TAATATTATATATATA
1 TAATATTATATATATA
11564 TA
1 TA
11566 TGTATCTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 5 0.31
16 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAATATTATATATATA
Found at i:11938 original size:2 final size:2
Alignment explanation
Indices: 11931--11977 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
11921 CATCATTTAA
*
11931 AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11973 AT AT A
1 AT AT A
11978 GATTGTGAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:13511 original size:22 final size:20
Alignment explanation
Indices: 13465--13533 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
13455 TACATAAGAC
*
13465 TTTTTATTATAAAATTTATA
1 TTTTTATAATAAAATTTATA
*
13485 TTTTTATAATATAATTTTATA
1 TTTTTATAATA-AAATTTATA
*
13506 TATTTTATAA-AAATAGTTATA
1 T-TTTTATAATAAA-ATTTATA
*
13527 ATTTTAT
1 TTTTTAT
13534 TTTACTAGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
20 18 0.44
21 15 0.37
22 8 0.20
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (20 bp):
TTTTTATAATAAAATTTATA
Found at i:14019 original size:16 final size:17
Alignment explanation
Indices: 14000--14043 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
13990 AACTAAAATG
14000 ATTTAAATTCGAAT-TA
1 ATTTAAATTCGAATATA
*
14016 ATTTAATTTCG-ATATA
1 ATTTAAATTCGAATATA
14032 A-TTAAATTCGAA
1 ATTTAAATTCGAA
14044 CAATCAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (17 bp):
ATTTAAATTCGAATATA
Found at i:16348 original size:2 final size:2
Alignment explanation
Indices: 16341--16376 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
16331 ACAATCTGAG
16341 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16377 ATTTGTGCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16565 original size:18 final size:17
Alignment explanation
Indices: 16542--16585 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
16532 TTATATAAAT
16542 AATATAAAAAATAATTAA
1 AATATAAAAAAT-ATTAA
*
16560 AATATAATATAATATTAA
1 AATATAA-AAAATATTAA
16578 AATATAAA
1 AATATAAA
16586 TATTTTGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 1 0.04
18 19 0.79
19 4 0.17
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AATATAAAAAATATTAA
Done.