Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold317
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: 948703
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 33011 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:872914 original size:12 final size:13
Alignment explanation
Indices: 872897--872930 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
872887 GGATTACAAG
872897 TTTCCATTTTC-A
1 TTTCCATTTTCTA
872909 TTTCCA-TTTCTA
1 TTTCCATTTTCTA
872921 TTTCCATTTT
1 TTTCCATTTT
872931 TCGAAACCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 4 0.20
12 13 0.65
13 3 0.15
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTCCATTTTCTA
Found at i:890815 original size:15 final size:15
Alignment explanation
Indices: 890795--890828 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
890785 CCTGAAGGTC
*
890795 AACTTTAGATTTATA
1 AACTTTAAATTTATA
*
890810 AACTTTAAATTTATC
1 AACTTTAAATTTATA
890825 AACT
1 AACT
890829 GCTTCATCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.03, T:0.44
Consensus pattern (15 bp):
AACTTTAAATTTATA
Found at i:899435 original size:19 final size:19
Alignment explanation
Indices: 899393--899436 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
899383 TTTCTCTCTC
*
899393 TTTTTT-TAATTTTTATAA
1 TTTTTTATAATTTTAATAA
* *
899411 TGTTTTATAATTTTAATTA
1 TTTTTTATAATTTTAATAA
899430 TTTTTTA
1 TTTTTTA
899437 AATGTCTATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTTTTATAATTTTAATAA
Found at i:905344 original size:63 final size:63
Alignment explanation
Indices: 905269--905388 Score: 195
Period size: 63 Copynumber: 1.9 Consensus size: 63
905259 GGCCATATGA
**
905269 CTTGCCCGTATGACCCAAATCCAAAGTCAATGAGTTACATGGCCTGGACACATGCCTTTGTGG
1 CTTGCCCGTATGACCCAAATCCAAAGTCAATGAGTTACACAGCCTGGACACATGCCTTTGTGG
* * *
905332 CTTGCCCGTATGACCCAAATCCGAAGTCAGTGAGTTACACAGCCTGGATACATGCCT
1 CTTGCCCGTATGACCCAAATCCAAAGTCAATGAGTTACACAGCCTGGACACATGCCT
905389 GTGTAACCCA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 52 1.00
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (63 bp):
CTTGCCCGTATGACCCAAATCCAAAGTCAATGAGTTACACAGCCTGGACACATGCCTTTGTGG
Found at i:914142 original size:17 final size:17
Alignment explanation
Indices: 914120--914183 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
914110 AATCTAAGAG
914120 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
914137 TTCTAATTGTGT-CTTAGAG
1 TTCTAATTGTATAC--AG-C
*
914156 TTCTAATTGTATACATC
1 TTCTAATTGTATACAGC
*
914173 TTTTAATTGTA
1 TTCTAATTGTA
914184 GCCTTTGATG
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
16 1 0.03
17 21 0.57
18 3 0.08
19 11 0.30
20 1 0.03
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.48
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:914453 original size:48 final size:48
Alignment explanation
Indices: 914388--914481 Score: 152
Period size: 48 Copynumber: 2.0 Consensus size: 48
914378 GAGGGAATTT
* *
914388 TGTTGAATCCTTTATCATTGCAAGTTAGGCCGACTTAGGCGTTTTTGC
1 TGTTGAATCCTTTATCATTACAAGTTAGGCCGACTTAGGCATTTTTGC
* *
914436 TGTTGAATCCTTTATCATTACGAGTTAGGCTGACTTAGGCATTTTT
1 TGTTGAATCCTTTATCATTACAAGTTAGGCCGACTTAGGCATTTTT
914482 AAGCAAAGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.41
Consensus pattern (48 bp):
TGTTGAATCCTTTATCATTACAAGTTAGGCCGACTTAGGCATTTTTGC
Found at i:915635 original size:31 final size:31
Alignment explanation
Indices: 915600--915665 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
915590 CTGTGATGGT
915600 CCACATATGATCAAGGACTGCCCAAAGAAGG
1 CCACATATGATCAAGGACTGCCCAAAGAAGG
915631 CCACATATGATCAAGGACTGCCCAAAGAAGG
1 CCACATATGATCAAGGACTGCCCAAAGAAGG
915662 CCAC
1 CCAC
915666 TCTCACGGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.38, C:0.29, G:0.21, T:0.12
Consensus pattern (31 bp):
CCACATATGATCAAGGACTGCCCAAAGAAGG
Found at i:919244 original size:17 final size:17
Alignment explanation
Indices: 919222--919285 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
919212 AATCTTAGAG
919222 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
919239 TTCTAATTGTGT-CTTAGAG
1 TTCTAATTGTATAC--AG-C
*
919258 TTCTAATTGTATACATC
1 TTCTAATTGTATACAGC
*
919275 TTTTAATTGTA
1 TTCTAATTGTA
919286 GCCTTTGATG
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
16 1 0.03
17 21 0.57
18 3 0.08
19 11 0.30
20 1 0.03
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.48
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:919261 original size:36 final size:36
Alignment explanation
Indices: 919214--919284 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
919204 GATTATGTAA
919214 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
* *
919250 TCTTAGAGTTCTAATTGTATACATCTTTTAATTGT
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGT
919285 AGCCTTTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.25, C:0.13, G:0.14, T:0.48
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
Found at i:919263 original size:19 final size:19
Alignment explanation
Indices: 919213--919269 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
919203 TGATTATGTA
919213 ATCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
*
919232 ATAC--AG-CTTCTAATTGT
1 AT-CTTAGAGTTCTAATTGT
*
919249 GTCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
919268 AT
1 AT
919270 ACATCTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
16 1 0.03
17 11 0.37
18 4 0.13
19 13 0.43
20 1 0.03
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (19 bp):
ATCTTAGAGTTCTAATTGT
Found at i:919564 original size:48 final size:48
Alignment explanation
Indices: 919489--919583 Score: 172
Period size: 48 Copynumber: 2.0 Consensus size: 48
919479 TGAGGGAATT
919489 CTGTTGAATCCTTTATCATTGCAAGTTAGGCCGACTTAGGCGTTTTTG
1 CTGTTGAATCCTTTATCATTGCAAGTTAGGCCGACTTAGGCGTTTTTG
* *
919537 CTGTTGAATCCTTTATCATTGCGAGTTAGGCTGACTTAGGCGTTTTT
1 CTGTTGAATCCTTTATCATTGCAAGTTAGGCCGACTTAGGCGTTTTT
919584 AAGCAAAGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.41
Consensus pattern (48 bp):
CTGTTGAATCCTTTATCATTGCAAGTTAGGCCGACTTAGGCGTTTTTG
Found at i:919846 original size:16 final size:16
Alignment explanation
Indices: 919821--919873 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
919811 ATAATTAACA
919821 TAAAGAAATA-TATATT
1 TAAA-AAATACTATATT
919837 TAAAACAATACT-TA-T
1 TAAAA-AATACTATATT
*
919852 T-AAAAATATTATATT
1 TAAAAAATACTATATT
919867 TAAAAAA
1 TAAAAAA
919874 ATAAATATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
13 5 0.16
14 5 0.16
15 5 0.16
16 15 0.48
17 1 0.03
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (16 bp):
TAAAAAATACTATATT
Found at i:919881 original size:16 final size:16
Alignment explanation
Indices: 919821--919883 Score: 60
Period size: 15 Copynumber: 4.1 Consensus size: 16
919811 ATAATTAACA
*
919821 TAAAGAAATATATATT
1 TAAAAAAATATATATT
*
919837 TAAAACAATACT-TA-T
1 TAAAAAAATA-TATATT
*
919852 TAAAAATAT-TATATT
1 TAAAAAAATATATATT
*
919867 TAAAAAAATAAATATT
1 TAAAAAAATATATATT
919883 T
1 T
919884 TTAAAAGAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
13 1 0.03
14 2 0.05
15 17 0.46
16 16 0.43
17 1 0.03
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (16 bp):
TAAAAAAATATATATT
Found at i:923981 original size:28 final size:27
Alignment explanation
Indices: 923933--923989 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
923923 AATGTTCAAA
*
923933 TATTTACAATTTATTTTATTTTTTTGTT
1 TATTTACAATTTATTTAATTTTTTT-TT
923961 TATTATACAATTT-TTTAATTTTTTTTT
1 TATT-TACAATTTATTTAATTTTTTTTT
923988 TA
1 TA
923990 GAATTACAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 4 0.15
28 15 0.56
29 8 0.30
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.70
Consensus pattern (27 bp):
TATTTACAATTTATTTAATTTTTTTTT
Found at i:925934 original size:23 final size:22
Alignment explanation
Indices: 925908--925951 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
925898 TTATTATATA
925908 AAAT-AAAAAAATTTAACATTTTT
1 AAATCAAAAAAA-TTAA-ATTTTT
*
925931 AAATCAAAATAATTAAATTTT
1 AAATCAAAAAAATTAAATTTT
925952 AAAAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
23 8 0.42
24 6 0.32
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (22 bp):
AAATCAAAAAAATTAAATTTTT
Found at i:931004 original size:26 final size:26
Alignment explanation
Indices: 930975--931027 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
930965 CTGTTGTCAA
930975 TCACATAGTTCAGATTCTAGAGATGG
1 TCACATAGTTCAGATTCTAGAGATGG
931001 TCACATAGTTCAGATTCTAGAGATGG
1 TCACATAGTTCAGATTCTAGAGATGG
931027 T
1 T
931028 TACTAACTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (26 bp):
TCACATAGTTCAGATTCTAGAGATGG
Found at i:932243 original size:3 final size:3
Alignment explanation
Indices: 932235--932278 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
932225 GTTGGTTCAC
932235 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
932279 AGTTAATGCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:932491 original size:30 final size:32
Alignment explanation
Indices: 932437--932500 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 32
932427 TAGTAAAAGT
* *
932437 AAAATTGTATTTTAGTCTTTTTAAAAATGATA
1 AAAATTGTATTTTAATCATTTTAAAAATGATA
*
932469 AAAATT-TATTTTAAT-ATTTTAAAAATTATA
1 AAAATTGTATTTTAATCATTTTAAAAATGATA
932499 AA
1 AA
932501 GATATAGGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 15 0.52
31 8 0.28
32 6 0.21
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (32 bp):
AAAATTGTATTTTAATCATTTTAAAAATGATA
Found at i:932844 original size:3 final size:3
Alignment explanation
Indices: 932836--932885 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
932826 ATTCACCTAT
932836 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
932884 TT
1 TT
932886 TTTAGTGAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:937406 original size:45 final size:45
Alignment explanation
Indices: 937333--937429 Score: 115
Period size: 45 Copynumber: 2.2 Consensus size: 45
937323 TTTGACCAAG
* *
937333 CCTGCTCCAAACCCGCATCTACAAGTCCAGCA-ATTAAAGCCTGCC
1 CCTGCTCCAAACCCGCAGCTACAAGTCCAGCAGA-TAAAGCCCGCC
* * * * *
937378 CCTGCTCCAATCCTGCAGCTCCAGGTCCAGCAGATAAAGCCCGCT
1 CCTGCTCCAAACCCGCAGCTACAAGTCCAGCAGATAAAGCCCGCC
937423 CCTGCTC
1 CCTGCTC
937430 TAGGCCCGTA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
45 43 0.98
46 1 0.02
ACGTcount: A:0.24, C:0.41, G:0.16, T:0.19
Consensus pattern (45 bp):
CCTGCTCCAAACCCGCAGCTACAAGTCCAGCAGATAAAGCCCGCC
Found at i:940880 original size:3 final size:3
Alignment explanation
Indices: 940872--940897 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
940862 TTTAATCATA
940872 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
940898 ACGTAAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:941450 original size:21 final size:21
Alignment explanation
Indices: 941424--941477 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
941414 CAGCGGTGGT
*
941424 GGTGAGATTAGTTACTGTAGC
1 GGTGAGATTAGATACTGTAGC
*
941445 GGTGAGATTGGATACTGTAGC
1 GGTGAGATTAGATACTGTAGC
*
941466 AGTGAGATTAGA
1 GGTGAGATTAGA
941478 AACAATGGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.07, G:0.35, T:0.30
Consensus pattern (21 bp):
GGTGAGATTAGATACTGTAGC
Found at i:941816 original size:15 final size:16
Alignment explanation
Indices: 941784--941826 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
941774 TATATTTATT
941784 AAATTATATAAAATTAA
1 AAATTAT-TAAAATTAA
*
941801 ATATTATTAAAA-TAA
1 AAATTATTAAAATTAA
*
941816 AAAGTATTAAA
1 AAATTATTAAA
941827 TAAGTATAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 12 0.52
16 5 0.22
17 6 0.26
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (16 bp):
AAATTATTAAAATTAA
Found at i:943136 original size:2 final size:2
Alignment explanation
Indices: 943129--943153 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
943119 CTCGTGCTTT
943129 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
943154 TAGATTATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:943938 original size:21 final size:21
Alignment explanation
Indices: 943914--943960 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
943904 TGTTCAAAAT
* *
943914 GTCAA-TCCTATGAATAATGGG
1 GTCAAGTCC-ATGAACAATGGA
943935 GTCAAGTCCATGAACAATGGA
1 GTCAAGTCCATGAACAATGGA
943956 GTCAA
1 GTCAA
943961 ATAATGAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.23
Consensus pattern (21 bp):
GTCAAGTCCATGAACAATGGA
Found at i:945256 original size:73 final size:72
Alignment explanation
Indices: 945107--945278 Score: 211
Period size: 73 Copynumber: 2.4 Consensus size: 72
945097 ATAAAAAGCA
* * * *
945107 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGACCTATGACACCATTTCCCGAGCTTT
1 TTAGCGGCGTTTTTGAGAAAGCGTCGCAAAAAACATAAGACCAACGACACCATTTCCCGAGCTTT
945172 CGGGGAT
66 CGGGGAT
* * * ***
945179 TTAGCGGCGTTTCTGAGAAAGCGTCGCAAAAAAACATAAGCCCAACGACGA-CGTTTTGTGAGCT
1 TTAGCGGCGTTTTTGAGAAAGCGTCGC-AAAAAACATAAGACCAACGAC-ACCATTTCCCGAGCT
*
945243 TTCGGGGGT
64 TTCGGGGAT
*
945252 TTAGCGGCGTTTTTAAGAAAGCGTCGC
1 TTAGCGGCGTTTTTGAGAAAGCGTCGC
945279 TAATGCTCTG
Statistics
Matches: 85, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
72 25 0.29
73 59 0.69
74 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (72 bp):
TTAGCGGCGTTTTTGAGAAAGCGTCGCAAAAAACATAAGACCAACGACACCATTTCCCGAGCTTT
CGGGGAT
Found at i:945327 original size:114 final size:114
Alignment explanation
Indices: 945178--945716 Score: 776
Period size: 114 Copynumber: 4.7 Consensus size: 114
945168 CTTTCGGGGA
* * * *
945178 TTTAGCGGCGTTTCTGAGAAAGCGTCGCAAAAAAACATAAGCCCAACGACGACGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCT
* * *
945243 TTCGGGGGTTTAGCGGCGTTTTTAAGAAAGCGTCGCTAATGCTCTGGGC
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
945292 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCT
* * * *
945357 TTTGGAGATTTAGCTGCGTTTTT-AGTAAAGCGCCACTAATGCTCAGGGC
66 TTCGGGGATTTAGCGGCGTTTTTAAG-AAAGCGCCGCTAATGCTCAGGGC
* ** * * * *
945406 TTTAGTGGCGCTTCCTCA-AAAACGCCGCAAGAAAACCTAAGCCCAACGACGCCGTTTTGTTAGC
1 TTTAGCGGCG-TTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGC
* *
945470 TTTCAGGGATTTAGCGGCGTTTTTTAAGAAAGTGCCGCTAATGCTCAGGGC
65 TTTCGGGGATTTAGCGGCG-TTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
** *
945521 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGATGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCT
* *
945586 TTCGGGAATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGTTCAGGGC
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
** *
945635 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAATTCTAAGCCCAACGACGCCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCT
*
945700 TTCAGGGATTTAGCGGC
66 TTCGGGGATTTAGCGGC
945717 CAAAAATGCT
Statistics
Matches: 376, Mismatches: 44, Indels: 10
0.87 0.10 0.02
Matches are distributed among these distances:
113 2 0.01
114 276 0.73
115 96 0.26
116 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (114 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCT
TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
Found at i:945618 original size:229 final size:227
Alignment explanation
Indices: 945178--945716 Score: 760
Period size: 229 Copynumber: 2.4 Consensus size: 227
945168 CTTTCGGGGA
* * * * * *
945178 TTTAGCGGCGTTTCTGAGAAAGCGTCGCAAAAAAACATAAGCCCAACGACGACGTTTTGTGAGCT
1 TTTAGCGGCGTTCCTCAGAAAACGCCGC-AAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCT
* * * *
945243 TTCGGGGGTTTAGCGGCGTTTTTAAGAAAGCGTCGCTAATGCTCTGGGCTTTAGCGGCGTTTTTG
65 TTCAGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTG
* * * *
945308 AGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCTTTTGGAGATTTAGCTG
130 AGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGACGTTTTCTGAGCTTTGGGAGATTTAGCGG
945373 CGTTTTTAGTAAAGCGCCACTAATGCTCAGGGC
195 CGTTTTTAGTAAAGCGCCACTAATGCTCAGGGC
* *
945406 TTTAGTGGCGCTTCCTCA-AAAACGCCGCAAGAAAACCTAAGCCCAACGACGCCGTTTTGTTAGC
1 TTTAGCGGCG-TTCCTCAGAAAACGCCGCAA-AAAACCTAAGCCCAACGACGCCGTTTTGTGAGC
*
945470 TTTCAGGGATTTAGCGGCGTTTTTTAAGAAAGTGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTT
64 TTTCAGGGATTTAGCGGCG-TTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTT
*
945535 TGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGATGTTTTCTGAGCTTTCGGGA-ATTTAG
128 TGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGACGTTTTCTGAGCTTT-GGGAGATTTAG
* *
945599 CGGCGTTTTTAAG-AAAGCGCCGCTAATGTTCAGGGC
192 CGGCGTTTTT-AGTAAAGCGCCACTAATGCTCAGGGC
** * * * *
945635 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAATTCTAAGCCCAACGACGCCGTTTTCTGAGCT
1 TTTAGCGGCGTTCCTCAGAAAACGCCGCAAAAAA-CCTAAGCCCAACGACGCCGTTTTGTGAGCT
945700 TTCAGGGATTTAGCGGC
65 TTCAGGGATTTAGCGGC
945717 CAAAAATGCT
Statistics
Matches: 276, Mismatches: 28, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
227 2 0.01
228 72 0.26
229 197 0.71
230 5 0.02
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (227 bp):
TTTAGCGGCGTTCCTCAGAAAACGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCTT
TCAGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGA
GAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGACGTTTTCTGAGCTTTGGGAGATTTAGCGGC
GTTTTTAGTAAAGCGCCACTAATGCTCAGGGC
Done.