Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2424
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: 23485
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:142 original size:84 final size:85
Alignment explanation
Indices: 1--197 Score: 303
Period size: 84 Copynumber: 2.4 Consensus size: 85
* *
1 AGGGTAACAGGCTAAAATTTACAGATCCTGGCTCTCCGAGCAGTGGTGGAGCAGGTCGAAGACTC
1 AGGGTAACAGGCTAAAATTTACAGATCTTAGCTCTCCGAGCAGTGGTGGAGCAGGTCGAAGACTC
* * *
66 G-CTT-AGCTCTCTAAGCAGT
66 GCCTTAACCCCT-TAAGCAAT
*
85 AGGGTAACAGGCTAAAATTTACAGATCTTAGCTCTCTGAGCAGTGGTGGAGCAGGTCGAAGACTC
1 AGGGTAACAGGCTAAAATTTACAGATCTTAGCTCTCCGAGCAGTGGTGGAGCAGGTCGAAGACTC
150 GCCTTAACCCCTTAAGCAAT
66 GCCTTAACCCCTTAAGCAAT
170 AGGGTAA-AGGCTAAAA-TTACAGATCTTA
1 AGGGTAACAGGCTAAAATTTACAGATCTTA
198 TTTTCGTTGA
Statistics
Matches: 105, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
83 12 0.11
84 72 0.69
85 17 0.16
86 4 0.04
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (85 bp):
AGGGTAACAGGCTAAAATTTACAGATCTTAGCTCTCCGAGCAGTGGTGGAGCAGGTCGAAGACTC
GCCTTAACCCCTTAAGCAAT
Found at i:480 original size:27 final size:28
Alignment explanation
Indices: 435--487 Score: 83
Period size: 27 Copynumber: 1.9 Consensus size: 28
425 TTAAACACCC
435 CTAAACCGACCACTAACTCCATCACCTA
1 CTAAACCGACCACTAACTCCATCACCTA
463 CTAAACC-ATCCACT-ACTCCATCACC
1 CTAAACCGA-CCACTAACTCCATCACC
488 CCAACCTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.34, C:0.45, G:0.02, T:0.19
Consensus pattern (28 bp):
CTAAACCGACCACTAACTCCATCACCTA
Found at i:512 original size:18 final size:18
Alignment explanation
Indices: 491--546 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
481 CATCACCCCA
491 ACCTACTAAACATCCACT
1 ACCTACTAAACATCCACT
* * *
509 ACCT-C-CATCACCCCAC-
1 ACCTACTAAACA-TCCACT
525 ACCTACTAAACATCCACT
1 ACCTACTAAACATCCACT
543 ACCT
1 ACCT
547 CCATCACCCC
Statistics
Matches: 28, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
16 7 0.25
17 10 0.36
18 11 0.39
ACGTcount: A:0.34, C:0.46, G:0.00, T:0.20
Consensus pattern (18 bp):
ACCTACTAAACATCCACT
Found at i:534 original size:34 final size:34
Alignment explanation
Indices: 457--556 Score: 177
Period size: 34 Copynumber: 3.0 Consensus size: 34
447 CTAACTCCAT
457 CACCTACTAAACCATCCACTA-CTCCATCACCCCA
1 CACCTACTAAA-CATCCACTACCTCCATCACCCCA
491 -ACCTACTAAACATCCACTACCTCCATCACCCCA
1 CACCTACTAAACATCCACTACCTCCATCACCCCA
524 CACCTACTAAACATCCACTACCTCCATCACCCC
1 CACCTACTAAACATCCACTACCTCCATCACCCC
557 CACTAACTCC
Statistics
Matches: 64, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
32 9 0.14
33 23 0.36
34 32 0.50
ACGTcount: A:0.32, C:0.50, G:0.00, T:0.18
Consensus pattern (34 bp):
CACCTACTAAACATCCACTACCTCCATCACCCCA
Found at i:559 original size:18 final size:18
Alignment explanation
Indices: 504--573 Score: 65
Period size: 18 Copynumber: 4.0 Consensus size: 18
494 TACTAAACAT
504 CCACTACCTCCATCA-CC
1 CCACTACCTCCATCACCC
* * **
521 CCAC-ACCTAC-TAAACAT
1 CCACTACCTCCAT-CACCC
538 CCACTACCTCCATCACCC
1 CCACTACCTCCATCACCC
*
556 CCACTAACTCCATCACCC
1 CCACTACCTCCATCACCC
574 TACTTGTTAT
Statistics
Matches: 40, Mismatches: 9, Indels: 7
0.71 0.16 0.12
Matches are distributed among these distances:
15 1 0.03
16 6 0.15
17 8 0.20
18 24 0.60
19 1 0.03
ACGTcount: A:0.29, C:0.54, G:0.00, T:0.17
Consensus pattern (18 bp):
CCACTACCTCCATCACCC
Found at i:978 original size:57 final size:57
Alignment explanation
Indices: 859--971 Score: 133
Period size: 57 Copynumber: 2.0 Consensus size: 57
849 TTTTATTTTG
* * *
859 TTATTTTACTGTTAATTAATTATTTGAGCTTTATTCTCATTATTTTTATATTTTATTA
1 TTATTTTACTATTAATTAATTATTTGAGC-TTATTCTCATTATTATTATATTATATTA
*
917 TTATTTT-CTATTAATTTAATTAATTTGAG-TTATGTTTCA-TATTATTATATTATAT
1 TTATTTTACTATTAA-TTAATT-ATTTGAGCTTAT-TCTCATTATTATTATATTATAT
972 ATTTATTATG
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
57 24 0.50
58 17 0.35
59 7 0.15
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.61
Consensus pattern (57 bp):
TTATTTTACTATTAATTAATTATTTGAGCTTATTCTCATTATTATTATATTATATTA
Found at i:980 original size:19 final size:21
Alignment explanation
Indices: 955--999 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
945 GTTATGTTTC
*
955 ATATTAT-TATAT-TATATAT
1 ATATTATGTAAATATATATAT
*
974 TTATTATGTAAATATATATAT
1 ATATTATGTAAATATATATAT
995 ATATT
1 ATATT
1000 CTTAAGCGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 6 0.29
20 4 0.19
21 11 0.52
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
ATATTATGTAAATATATATAT
Found at i:1219 original size:21 final size:21
Alignment explanation
Indices: 1186--1236 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1176 CTATTATCCC
** *
1186 CATATTTAATGTTATCGTCAA
1 CATATTTTTTGTTATCATCAA
* *
1207 CATATTTTTTGTTATTATCAT
1 CATATTTTTTGTTATCATCAA
1228 CATATTTTT
1 CATATTTTT
1237 AATATTATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.27, C:0.12, G:0.06, T:0.55
Consensus pattern (21 bp):
CATATTTTTTGTTATCATCAA
Found at i:1910 original size:19 final size:19
Alignment explanation
Indices: 1874--1912 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1864 TATAATATTA
*
1874 AAAATATGATGATAATAAC
1 AAAATATGATGACAATAAC
* *
1893 AAAATATGTTGACGATAAC
1 AAAATATGATGACAATAAC
1912 A
1 A
1913 TTAAATATGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.08, G:0.13, T:0.26
Consensus pattern (19 bp):
AAAATATGATGACAATAAC
Found at i:2490 original size:18 final size:18
Alignment explanation
Indices: 2467--2502 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2457 ATAACAAGTA
*
2467 GGGTGATGGAGTTAGTGG
1 GGGTGATGGAGGTAGTGG
2485 GGGTGATGGAGGTAGTGG
1 GGGTGATGGAGGTAGTGG
2503 ATGGTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.58, T:0.25
Consensus pattern (18 bp):
GGGTGATGGAGGTAGTGG
Found at i:2580 original size:36 final size:37
Alignment explanation
Indices: 2481--2588 Score: 188
Period size: 36 Copynumber: 3.0 Consensus size: 37
2471 GATGGAGTTA
2481 GTGGGGGTGATGGAGGTAGTGGATGGTTTAGTAGGGT
1 GTGGGGGTGATGGAGGTAGTGGATGGTTTAGTAGGGT
2518 GT-GGGGTG-TGGAGGTAGTGGAT-GTTTAGTAGGGT
1 GTGGGGGTGATGGAGGTAGTGGATGGTTTAGTAGGGT
2552 GTGGGGGTGATGGAGGTAGT-GATGGTTTAGTAGGGT
1 GTGGGGGTGATGGAGGTAGTGGATGGTTTAGTAGGGT
2588 G
1 G
2589 ATGGAGTTAG
Statistics
Matches: 68, Mismatches: 0, Indels: 7
0.91 0.00 0.09
Matches are distributed among these distances:
34 14 0.21
35 23 0.34
36 29 0.43
37 2 0.03
ACGTcount: A:0.16, C:0.00, G:0.54, T:0.31
Consensus pattern (37 bp):
GTGGGGGTGATGGAGGTAGTGGATGGTTTAGTAGGGT
Found at i:2615 original size:28 final size:28
Alignment explanation
Indices: 2555--2616 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
2545 GTAGGGTGTG
2555 GGGGTGATGGAGGTAGTGATGGTTTAGT
1 GGGGTGATGGAGGTAGTGATGGTTTAGT
* * *
2583 AGGGTGATGGAGTTAGTGGTCGGTTTA-T
1 GGGGTGATGGAGGTAGTGAT-GGTTTAGT
2611 GGGGTG
1 GGGGTG
2617 TTTAATTGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 23 0.79
29 6 0.21
ACGTcount: A:0.16, C:0.02, G:0.50, T:0.32
Consensus pattern (28 bp):
GGGGTGATGGAGGTAGTGATGGTTTAGT
Found at i:2982 original size:85 final size:85
Alignment explanation
Indices: 2851--3409 Score: 650
Period size: 85 Copynumber: 6.6 Consensus size: 85
2841 CAACGAAAAT
*
2851 AAGATCTGT-AATTTTAGCCTGTTACCCTATTGCTTA-AGGGGTTAAGGCGAGTCTTCGACCTGC
1 AAGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGA-GGGTTAAGGCGAGTCTTCGACCTGC
* * *
2914 TCCACCACTGCTCAGAGAGCT
65 TCCACCACTGCTCGGCGAGCC
* * * * *
2935 AAGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGAGAGCTAAGGTGAGTCTTTGACTTGCT
1 AAGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGAGGGTTAAGGCGAGTCTTCGACCTGCT
*
3000 CCACCACTGCTTGGCGAGCCC
66 CCACCACTGCTCGGCGAG-CC
* * * *
3021 AAG-TCTGTAAACTTTAGCCTGTTACCCTACTGATTAGGGGGTTAAGGCGAGTCTTCGACCTACT
1 AAGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGAGGGTTAAGGCGAGTCTTCGACCTGCT
*
3085 CTACCACTGCTCGGCGAGCC
66 CCACCACTGCTCGGCGAGCC
* * * * *
3105 CAGATTTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGC-ATGTATCTTTGATCT
1 AAGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGAGGGTTAAGGCGA-G--TCTTCGACCT
*
3169 GCTCCGCCACTGCTCGGCGAGCCC
63 GCTCCACCACTGCTCGGCGAG-CC
* * *
3193 AAG-TCTGTAAACTTTAGCCTGTTACCCTACTGCTTAGAAGGTTAAGGCGAGTCTTCGACCTACT
1 AAGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGAGGGTTAAGGCGAGTCTTCGACCTGCT
* * *
3257 CCGCCACTACTAGGCGAGCC
66 CCACCACTGCTCGGCGAGCC
* * * * * *
3277 CAGATCTGTACATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGTGTATCTTTGATCTG
1 AAGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGAGGGTTAAGGCGAG--TCTTCGACCTG
* *
3342 CTCCGCCACTGCT-TGCGAGCC
64 CTCCACCACTGCTCGGCGAGCC
* *
3363 CAGATCTGTAAATTTTAGCCTGATACCCTACTG-TT--AGGGTTAAGGCG
1 AAGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGAGGGTTAAGGCG
3410 TGTATCTTTG
Statistics
Matches: 409, Mismatches: 54, Indels: 25
0.84 0.11 0.05
Matches are distributed among these distances:
83 11 0.03
84 18 0.04
85 244 0.60
86 43 0.11
87 88 0.22
88 5 0.01
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (85 bp):
AAGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGAGGGTTAAGGCGAGTCTTCGACCTGCT
CCACCACTGCTCGGCGAGCC
Found at i:3241 original size:172 final size:170
Alignment explanation
Indices: 2855--3409 Score: 768
Period size: 172 Copynumber: 3.3 Consensus size: 170
2845 GAAAATAAGA
* * *
2855 TCTGT-AATTTTAGCCTGTTACCCTATTGCTTA-AGGGGTTAAGGCGAGTCTTCGACCTGCTCCA
1 TCTGTAAACTTTAGCCTGTTACCCTACTGCTTAGA-GGGTTAAGGCGAGTCTTCGACCTACTCCA
* * ** * * *
2918 CCACTGCTCAGAGAGCTAAGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGAGAGCTAAGG
65 CCACTGCTCGGCGAGCCCAGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
*
2983 -TG-AGTCTTTGA-CTTGCTCCACCACTGCTTGGCGAGCCCAAG
130 CTGTA-TCTTTGATC-TGCTCCGCCACTGC-TGGCGAGCCCAAG
* * *
3024 TCTGTAAACTTTAGCCTGTTACCCTACTGATTAGGGGGTTAAGGCGAGTCTTCGACCTACTCTAC
1 TCTGTAAACTTTAGCCTGTTACCCTACTGCTTAGAGGGTTAAGGCGAGTCTTCGACCTACTCCAC
*
3089 CACTGCTCGGCGAGCCCAGATTTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGC
66 CACTGCTCGGCGAGCCCAGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGC
3154 ATGTATCTTTGATCTGCTCCGCCACTGCTCGGCGAGCCCAAG
131 -TGTATCTTTGATCTGCTCCGCCACTGCT-GGCGAGCCCAAG
* *
3196 TCTGTAAACTTTAGCCTGTTACCCTACTGCTTAGAAGGTTAAGGCGAGTCTTCGACCTACTCCGC
1 TCTGTAAACTTTAGCCTGTTACCCTACTGCTTAGAGGGTTAAGGCGAGTCTTCGACCTACTCCAC
* * *
3261 CACTACTAGGCGAGCCCAGATCTGTACATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGC
66 CACTGCTCGGCGAGCCCAGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGC
*
3326 GTGTATCTTTGATCTGCTCCGCCACTGCTTGCGAGCCC-AG
131 -TGTATCTTTGATCTGCTCCGCCACTGCTGGCGAGCCCAAG
* *
3366 ATCTGTAAATTTTAGCCTGATACCCTACTG-TT--AGGGTTAAGGCG
1 -TCTGTAAACTTTAGCCTGTTACCCTACTGCTTAGAGGGTTAAGGCG
3410 TGTATCTTTG
Statistics
Matches: 349, Mismatches: 29, Indels: 17
0.88 0.07 0.04
Matches are distributed among these distances:
168 11 0.03
169 5 0.01
170 112 0.32
171 36 0.10
172 183 0.52
173 2 0.01
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (170 bp):
TCTGTAAACTTTAGCCTGTTACCCTACTGCTTAGAGGGTTAAGGCGAGTCTTCGACCTACTCCAC
CACTGCTCGGCGAGCCCAGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGC
TGTATCTTTGATCTGCTCCGCCACTGCTGGCGAGCCCAAG
Found at i:3317 original size:257 final size:255
Alignment explanation
Indices: 2852--3429 Score: 742
Period size: 257 Copynumber: 2.3 Consensus size: 255
2842 AACGAAAATA
* * *
2852 AGATCTGT-AATTTTAGCCTGTTACCCTATTGCTTAAGGGGTTAAGGC-G-AGTCTTCGACCTGC
1 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTT-AGGGGTTAAGGCTGTA-TCTTTGATCTGC
* *
2914 TCCACCACTGCTCAGAGAGCTAAGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGAGAGCT
64 TCCACCACTGCTCAGAGAGCCAAGATCTGTAAACTTTAGCCTGTTACCCTACTGCTTAGAGAGCT
* * * * * *
2979 AAGGTGAGTCTTTGACTTGCTCCACCACTGCTTGGCGAGCCCAAGTCTGTAAACTTTAGCCTGTT
129 AAGGCGAGTCTTCGACCTACTCCACCACTACTAGGCGAGCCCAAGTCTGTAAACTTTAGCCTGTT
*
3044 ACCCTACTGATTAGGGGGTTAAGGCGAG-TCTTCGACCTACTCTACCACTGCTCGGCGAGCCC
194 ACCCTACTGATTAGGGGGTTAAGGCGAGATCTTCGACCTACTCCACCACTGCT-GGCGAGCCC
*
3106 AGATTTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCATGTATCTTTGATCTGC
1 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTA-GGGGTTAAGGC-TGTATCTTTGATCTGC
* * *
3171 TCCGCCACTGCTCGGCGAGCCCAAG-TCTGTAAACTTTAGCCTGTTACCCTACTGCTTAGA-AGG
64 TCCACCACTGCTCAGAGAG-CCAAGATCTGTAAACTTTAGCCTGTTACCCTACTGCTTAGAGA-G
* * * *
3234 TTAAGGCGAGTCTTCGACCTACTCCGCCACTACTAGGCGAGCCC-AGATCTGTACATTTTAGCCT
127 CTAAGGCGAGTCTTCGACCTACTCCACCACTACTAGGCGAGCCCAAG-TCTGTAAACTTTAGCCT
* * * * * * *
3298 GTTACCCTACTGCTTAGGGGGTTAAGGCGTGTATCTTTGATCTGCTCCGCCACTGCTTGCGAGCC
191 GTTACCCTACTGATTAGGGGGTTAAGGCGAG-ATCTTCGACCTACTCCACCACTGCTGGCGAGCC
3363 C
255 C
* *
3364 AGATCTGTAAATTTTAGCCTGATACCCTACTG-TTA-GGGTTAAGGCGTGTATCTTTGATCTGTT
1 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGTTAAGGC-TGTATCTTTGATCTGCT
3427 CCA
65 CCA
3430 TTATTTCTTA
Statistics
Matches: 282, Mismatches: 32, Indels: 19
0.85 0.10 0.06
Matches are distributed among these distances:
254 8 0.03
255 64 0.23
256 3 0.01
257 145 0.51
258 43 0.15
259 19 0.07
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.31
Consensus pattern (255 bp):
AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGTTAAGGCTGTATCTTTGATCTGCTC
CACCACTGCTCAGAGAGCCAAGATCTGTAAACTTTAGCCTGTTACCCTACTGCTTAGAGAGCTAA
GGCGAGTCTTCGACCTACTCCACCACTACTAGGCGAGCCCAAGTCTGTAAACTTTAGCCTGTTAC
CCTACTGATTAGGGGGTTAAGGCGAGATCTTCGACCTACTCCACCACTGCTGGCGAGCCC
Found at i:3730 original size:128 final size:130
Alignment explanation
Indices: 3583--4035 Score: 528
Period size: 132 Copynumber: 3.5 Consensus size: 130
3573 CTGGTGTTTG
* *
3583 AATCTGCTCCATTGTCGATACATGGAGATAAGATCCGTGAAATTTGATCTATTCCACTCCTGCCA
1 AATCTGCTCCATTGCCGATACATGGAGATAAGATCCGTGAAATTTGATCTGTTCCACTCCTGCCA
* * * *
3648 GTGGATGAGATCTACTATATTTAGCCTGTTCTACTCCTGCTTAGTGGGATAA-CCTGGTGGTTTG
66 GTGGATGAGATCTACTATATTTAGCCTGTTCCACTCCTGCTCAGTGGGATAAGGCTGGTGG-CTG
3712 -
130 A
* *
3712 AAT-TGCTCCATTGCCGATACATGGAGATAAGAT-CGTCAAAATTTGATCTGCTCCACTCCTGCT
1 AATCTGCTCCATTGCCGATACATGGAGATAAGATCCGT-GAAATTTGATCTGTTCCACTCCTGC-
* * * * * * *
3775 CAGCGAAGATAAGATCTA-GA-GTTTAGCGTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGGTG
64 CAGTG--GATGAGATCTACTATATTTAGCCTGTTCCACTCCTGCTCAGTG-GGATAAGGCTGGTG
3838 GCTGA
126 GCTGA
* *
3843 AATCTGCTCCATTGCCGATACAT-GAGACAAGATCCGCTGAAATTTGATCTGTTCCACTCCTGTC
1 AATCTGCTCCATTGCCGATACATGGAGATAAGATCCG-TGAAATTTGATCTGTTCCACTCCTGCC
* * *
3907 AGTGGGATGAGATCTGCTATATTTAGCCTGTTCCACTCCTACTCAGTGGGATAAGGCTTGTGGCT
65 AGT-GGATGAGATCTACTATATTTAGCCTGTTCCACTCCTGCTCAGTGGGATAAGGCTGGTGGCT
3972 GA
129 GA
* * ** * *
3974 AATCTGCTCCATTGCC--TACATAGAGATAAGATTCGCCAAAATTTGATCTGCTCCGCTCCTGC
1 AATCTGCTCCATTGCCGATACATGGAGATAAGATCCG-TGAAATTTGATCTGTTCCACTCCTGC
4036 TCAGCGAAGA
Statistics
Matches: 274, Mismatches: 36, Indels: 27
0.81 0.11 0.08
Matches are distributed among these distances:
127 3 0.01
128 51 0.19
129 35 0.13
130 50 0.18
131 66 0.24
132 68 0.25
133 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (130 bp):
AATCTGCTCCATTGCCGATACATGGAGATAAGATCCGTGAAATTTGATCTGTTCCACTCCTGCCA
GTGGATGAGATCTACTATATTTAGCCTGTTCCACTCCTGCTCAGTGGGATAAGGCTGGTGGCTGA
Found at i:4088 original size:176 final size:176
Alignment explanation
Indices: 3881--4319 Score: 677
Period size: 176 Copynumber: 2.5 Consensus size: 176
3871 AAGATCCGCT
*
3881 GAAATTTGATCTGTTCCACTCCTGTCAGTGGGATGAGATCTGCTATATTTAGCCTGTTCCACTCC
1 GAAATTTGATCTGTTCCACTCCTGCCAGTGGGATGAGATCTGCTATATTTAGCCTGTTCCACTCC
*
3946 TACTCAGTGGGATAAGGCTTGTGGCTGAAATCTGCTCCATTGCC-TACATAGAGATAAGATTCGC
66 TGCTCAGTGGGATAAGGCTTGTGGCTGAAATCTGCTCCATTGCCATACATAGAGATAAGATTCGC
* *
4010 CAAAATTTGATCTGCTCCGCTCCTGCTCAGCGAAGATAAGATCTGTC
131 CAAAATTTGATCTGCTCCGCTCCTGATCAACGAAGATAA-ATCTGTC
*
4057 GAAATTTGATCTGTTCCACTCCAGCCAGTGGGATGAGATCTGCTATATTTAGCCTGCTT-CACTC
1 GAAATTTGATCTGTTCCACTCCTGCCAGTGGGATGAGATCTGCTATATTTAGCCTG-TTCCACTC
* * * * *
4121 TTGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGGTAAGATT
65 CTGCTCAGTG-GGATAAGGCTTGTGGCTGAAATCTGCTCCATTGCC-ATACATAGAGATAAGATT
*
4186 CGCCAAAATTTGATTTGCTCCGCTCCTGATCAACGAAGATAAATCTGTC
128 CGCCAAAATTTGATCTGCTCCGCTCCTGATCAACGAAGATAAATCTGTC
* * * * *
4235 GAAATTTGATATATTCCACTCGTGCCAGTAGGATGAGATCTGCTATATTTAGCCTATTCCACTCC
1 GAAATTTGATCTGTTCCACTCCTGCCAGTGGGATGAGATCTGCTATATTTAGCCTGTTCCACTCC
4300 TGCTCAGT-GGATAAGGCTTG
66 TGCTCAGTGGGATAAGGCTTG
4320 CCAAAATCTG
Statistics
Matches: 238, Mismatches: 20, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
176 77 0.32
177 37 0.16
178 70 0.29
179 54 0.23
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.31
Consensus pattern (176 bp):
GAAATTTGATCTGTTCCACTCCTGCCAGTGGGATGAGATCTGCTATATTTAGCCTGTTCCACTCC
TGCTCAGTGGGATAAGGCTTGTGGCTGAAATCTGCTCCATTGCCATACATAGAGATAAGATTCGC
CAAAATTTGATCTGCTCCGCTCCTGATCAACGAAGATAAATCTGTC
Found at i:5609 original size:17 final size:18
Alignment explanation
Indices: 5575--5612 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5565 TCTCCTTTGC
*
5575 TTTTATTTTCTTTCTCTT
1 TTTTATTTTCTCTCTCTT
*
5593 TTTTGTTTTCTCT-TCTT
1 TTTTATTTTCTCTCTCTT
5610 TTT
1 TTT
5613 CCTTTTCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTTATTTTCTCTCTCTT
Found at i:5621 original size:15 final size:15
Alignment explanation
Indices: 5574--5653 Score: 66
Period size: 15 Copynumber: 5.7 Consensus size: 15
5564 CTCTCCTTTG
*
5574 CTTTTATTTTCTTTCT
1 CTTTTCTTTT-TTTCT
*
5590 CTTTT-TTGTTTTCT
1 CTTTTCTTTTTTTCT
5604 C--TTC--TTTTTC-
1 CTTTTCTTTTTTTCT
5614 CTTTTCTTTTTTTCT
1 CTTTTCTTTTTTTCT
*
5629 CTTTCCTTTTTTTCTT
1 CTTTTCTTTTTTTC-T
5645 CTTTT-TTTT
1 CTTTTCTTTT
5654 AAGTGAAGTA
Statistics
Matches: 53, Mismatches: 4, Indels: 15
0.74 0.06 0.21
Matches are distributed among these distances:
10 1 0.02
11 5 0.09
12 5 0.09
14 12 0.23
15 20 0.38
16 10 0.19
ACGTcount: A:0.01, C:0.20, G:0.01, T:0.78
Consensus pattern (15 bp):
CTTTTCTTTTTTTCT
Found at i:5626 original size:25 final size:27
Alignment explanation
Indices: 5585--5652 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 27
5575 TTTTATTTTC
*
5585 TTTCTCTTTT-TTGTTTTCTC-TT-CTT
1 TTTC-CTTTTCTTTTTTTCTCTTTCCTT
5610 TTTCCTTTTCTTTTTTTCTCTTTCCTT
1 TTTCCTTTTCTTTTTTTCTCTTTCCTT
5637 TTT--TTCTTCTTTTTTT
1 TTTCCTT-TTCTTTTTTT
5653 TAAGTGAAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
24 5 0.13
25 15 0.39
26 12 0.32
27 6 0.16
ACGTcount: A:0.00, C:0.21, G:0.01, T:0.78
Consensus pattern (27 bp):
TTTCCTTTTCTTTTTTTCTCTTTCCTT
Found at i:5652 original size:14 final size:13
Alignment explanation
Indices: 5580--5653 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 13
5570 TTTGCTTTTA
*
5580 TTTTCTTTCTCTT
1 TTTTTTTTCTCTT
5593 TTTTGTTTTCTC-T
1 TTTT-TTTTCTCTT
* *
5606 TCTTTTTCCT-TT
1 TTTTTTTTCTCTT
5618 TCTTTTTTTCTCTT
1 T-TTTTTTTCTCTT
5632 TCCTTTTTTTCTTCTT
1 T--TTTTTTTC-TCTT
5648 TTTTTT
1 TTTTTT
5654 AAGTGAAGTA
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
12 7 0.14
13 15 0.30
14 14 0.28
15 9 0.18
16 5 0.10
ACGTcount: A:0.00, C:0.20, G:0.01, T:0.78
Consensus pattern (13 bp):
TTTTTTTTCTCTT
Found at i:5652 original size:29 final size:27
Alignment explanation
Indices: 5580--5653 Score: 73
Period size: 26 Copynumber: 2.7 Consensus size: 27
5570 TTTGCTTTTA
5580 TTTTCTTTC-TCTTTTTTGTTTTCTCTTC
1 TTTT-TTTCTTCTTTTTT-TTTTCTCTTC
* *
5608 -TTTTTCCTT-TTCTTTTTTTCTCTTTCC
1 TTTTTTTCTTCTTTTTTTTTTCTC-TT-C
5635 TTTTTTTCTTCTTTTTTTT
1 TTTTTTTCTTCTTTTTTTT
5654 AAGTGAAGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
25 7 0.19
26 10 0.27
27 5 0.14
28 8 0.22
29 7 0.19
ACGTcount: A:0.00, C:0.20, G:0.01, T:0.78
Consensus pattern (27 bp):
TTTTTTTCTTCTTTTTTTTTTCTCTTC
Found at i:8222 original size:21 final size:21
Alignment explanation
Indices: 8196--8240 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
8186 GCTGGCTCAT
*
8196 CATGTTGTTCTGTGACTCCAG
1 CATGTTGTTCTGGGACTCCAG
*
8217 CATGTTTTTCTGGGACTCCAG
1 CATGTTGTTCTGGGACTCCAG
8238 CAT
1 CAT
8241 TTGATCCCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (21 bp):
CATGTTGTTCTGGGACTCCAG
Found at i:11902 original size:126 final size:126
Alignment explanation
Indices: 11742--11985 Score: 425
Period size: 126 Copynumber: 1.9 Consensus size: 126
11732 GTTTTAGCCT
*
11742 TAAGAGGATATTCGAATATTCAAAACAAACAAAGAAAGTGAAACCCAGTACGTTAGGGCACGATT
1 TAAGAGGATATTCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATT
* *
11807 CTTCAAATTTTTTAAATACCGAAAATTGCCTTTATTATGAAAATTTTTGAGAGTGAACTGG
66 CTTCAAATTCTTTAAATACCGAAAATTGCCTTTATTATGAAAAATTTTGAGAGTGAACTGG
*
11868 TAAGAGGATATTCGAATATTCAAGACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATT
1 TAAGAGGATATTCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATT
* * *
11933 CTTCGAATTCTTTAAATACCGAACATTGCCTTTATTTTGAAAAATTTTGAGAG
66 CTTCAAATTCTTTAAATACCGAAAATTGCCTTTATTATGAAAAATTTTGAGAG
11986 AAGATCAATG
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
126 111 1.00
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.29
Consensus pattern (126 bp):
TAAGAGGATATTCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATT
CTTCAAATTCTTTAAATACCGAAAATTGCCTTTATTATGAAAAATTTTGAGAGTGAACTGG
Found at i:12847 original size:46 final size:46
Alignment explanation
Indices: 12790--13244 Score: 738
Period size: 46 Copynumber: 10.0 Consensus size: 46
12780 TTTGACATGA
* * * * * *
12790 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
*
12836 TGCCATGGTGTCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
12882 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
12928 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
12974 TGCCATGGTGTCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
13020 TGCCATGGTATCTTTCAACCATGG---TACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
13063 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
13109 TGCCATGGTGTCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* *
13155 TGCCATGATATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* * *
13201 TGTCATGGTATCTTTCAACCATGGTTTTACACATTTCATTTCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
13245 AGAGCACACT
Statistics
Matches: 387, Mismatches: 18, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
43 43 0.11
45 4 0.01
46 340 0.88
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.38
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:15714 original size:29 final size:30
Alignment explanation
Indices: 15657--15724 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
15647 CACCCTTAAA
* * * *
15657 ATATTTGCACTATTAGTCCTTTAACTTTTC
1 ATATTTACACTATTAATCCTTCAAATTTTC
*
15687 ATATTTACACT-TTAATCCTTCAAATTTTG
1 ATATTTACACTATTAATCCTTCAAATTTTC
15716 AGTATTTAC
1 A-TATTTAC
15725 TCTTGGGCCA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.28, C:0.18, G:0.06, T:0.49
Consensus pattern (30 bp):
ATATTTACACTATTAATCCTTCAAATTTTC
Found at i:16316 original size:11 final size:10
Alignment explanation
Indices: 16300--16334 Score: 52
Period size: 11 Copynumber: 3.3 Consensus size: 10
16290 ATATATTTAC
16300 ATAATAAATA
1 ATAATAAATA
16310 TATAATAAATA
1 -ATAATAAATA
16321 ATAATATAATA
1 ATAATA-AATA
16332 ATA
1 ATA
16335 TGAAACATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 6 0.26
11 17 0.74
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
ATAATAAATA
Found at i:16372 original size:63 final size:64
Alignment explanation
Indices: 16323--16443 Score: 160
Period size: 63 Copynumber: 1.9 Consensus size: 64
16313 AATAAATAAT
* *
16323 AATATAATAAT-ATGAAACAT-AA-CTCAAATTAATTAAATTAATAG-AAAATAATAAAAAAACA
1 AATATAAAAATAATGAAA-ATAAAGCTCAAATTAATTAAATTAACAGTAAAATAATAAAAAAACA
* * *
16384 AATATAAAAATAATGAGAATAAAGCTCAAATTAATTAATTTAACAGTAAAATAACAAAAA
1 AATATAAAAATAATGAAAATAAAGCTCAAATTAATTAAATTAACAGTAAAATAATAAAAA
16444 TAAAGAAAGG
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
61 12 0.24
62 7 0.14
63 20 0.39
64 12 0.24
ACGTcount: A:0.63, C:0.07, G:0.05, T:0.26
Consensus pattern (64 bp):
AATATAAAAATAATGAAAATAAAGCTCAAATTAATTAAATTAACAGTAAAATAATAAAAAAACA
Found at i:16813 original size:29 final size:29
Alignment explanation
Indices: 16751--16807 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
16741 GAGAGTGTGG
*
16751 GGGTGATGAAGGTAGTGGATGGTTTAGTA
1 GGGTGATGAAGGTAGTAGATGGTTTAGTA
*
16780 GGGTGATGGAGGTAGTAG-TCGGTTTAGT
1 GGGTGATGAAGGTAGTAGAT-GGTTTAGT
16808 GTGGTGTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 24 0.96
ACGTcount: A:0.21, C:0.02, G:0.46, T:0.32
Consensus pattern (29 bp):
GGGTGATGAAGGTAGTAGATGGTTTAGTA
Found at i:20149 original size:18 final size:18
Alignment explanation
Indices: 20126--20165 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
20116 AATTAAAGTG
*
20126 GACCTAGAAAAGGCTTAT
1 GACCTAGAAAAGGCGTAT
20144 GACCTAGAAAAGGCGTAT
1 GACCTAGAAAAGGCGTAT
20162 GACC
1 GACC
20166 GTATCTGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.25, T:0.17
Consensus pattern (18 bp):
GACCTAGAAAAGGCGTAT
Done.