Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold263
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: 1338270
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 10 of 10
Found at i:1282030 original size:33 final size:32
Alignment explanation
Indices: 1281940--1282034 Score: 109
Period size: 33 Copynumber: 2.9 Consensus size: 32
1281930 ATTCCGGAGC
* *
1281940 TGGTGCTGGGGTTGGTGACCAAGGATCAGGAAT
1 TGGTGCTGGGGCTGGTG-CCAAGGTTCAGGAAT
* * *
1281973 TGGTGTTGAGGCTGGTGCCCAAGGTTCTGGAAT
1 TGGTGCTGGGGCTGGTG-CCAAGGTTCAGGAAT
*
1282006 TGGTGCTGGGGCTGCTGCCGAAGGTTCAG
1 TGGTGCTGGGGCTGGTGCC-AAGGTTCAG
1282035 TTCGTGTTGG
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
32 2 0.04
33 49 0.96
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.26
Consensus pattern (32 bp):
TGGTGCTGGGGCTGGTGCCAAGGTTCAGGAAT
Found at i:1282318 original size:50 final size:50
Alignment explanation
Indices: 1282240--1282498 Score: 383
Period size: 50 Copynumber: 5.2 Consensus size: 50
1282230 AGTTGTTGCC
* * * *
1282240 ATTGTTGACTATCCTTCACTAACCTTTGACAATAGAGGGAGGTGACCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATA
* ** * *
1282290 ATTGTTGACGATTTTTCGTCAATCTTTGACAATAGAAGGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATA
* * *
1282340 ATTGTTGACGATTATTCACCAACCTTTGACAATAGAGAGAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATA
* *
1282390 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATA
*
1282440 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGGGAGGTGACCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATA
1282490 ATTGTTGAC
1 ATTGTTGAC
1282499 TCTAAGTATA
Statistics
Matches: 189, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 189 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATA
Found at i:1286968 original size:50 final size:50
Alignment explanation
Indices: 1286891--1286999 Score: 164
Period size: 50 Copynumber: 2.2 Consensus size: 50
1286881 AGTTATTGCC
* *
1286891 ATTGTTGACTATCCTTCACCAACCTTTGACAATAGAGGGAGGTGACCATA
1 ATTGTTGACGATCCTTCACCAACCTTTGACAATAGAAGGAGGTGACCATA
* * *
1286941 ATTGTTGACGATTCTTCACCAATCTTTGACAATAGAAGGAGGTGGCCATA
1 ATTGTTGACGATCCTTCACCAACCTTTGACAATAGAAGGAGGTGACCATA
*
1286991 ATTATTGAC
1 ATTGTTGAC
1287000 TCTAAGTATA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Consensus pattern (50 bp):
ATTGTTGACGATCCTTCACCAACCTTTGACAATAGAAGGAGGTGACCATA
Found at i:1288865 original size:55 final size:55
Alignment explanation
Indices: 1288800--1288911 Score: 152
Period size: 55 Copynumber: 2.0 Consensus size: 55
1288790 AAATAATATC
*
1288800 ATCTCATTAAAAATAAAATCATAAATATTAATTTTTAAAAACATTTAACAAAATG
1 ATCTCATTAAAAACAAAATCATAAATATTAATTTTTAAAAACATTTAACAAAATG
* * * * * **
1288855 ATCTCATTAAAAACAAAGTTATGAATATTAATTTTTAACAATATTTAATGAAATG
1 ATCTCATTAAAAACAAAATCATAAATATTAATTTTTAAAAACATTTAACAAAATG
1288910 AT
1 AT
1288912 ATCGTATGAT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.37
Consensus pattern (55 bp):
ATCTCATTAAAAACAAAATCATAAATATTAATTTTTAAAAACATTTAACAAAATG
Found at i:1289306 original size:23 final size:23
Alignment explanation
Indices: 1289272--1289329 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
1289262 AATAAGTTAT
1289272 TATATTTTTATTATAT-TTAAAA
1 TATATTTTTATTATATATTAAAA
*
1289294 TATATTTTTTATT-TATATTCAAA
1 TATA-TTTTTATTATATATTAAAA
*
1289317 TAAATTTTTATTA
1 TATATTTTTATTA
1289330 CAAATTTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 15 0.48
23 16 0.52
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (23 bp):
TATATTTTTATTATATATTAAAA
Found at i:1290151 original size:32 final size:32
Alignment explanation
Indices: 1290089--1290151 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
1290079 AGGAATATAC
** *
1290089 GTATCAAAATTTATATAATATAAATTATTTAT
1 GTATCAAAAAATATATAATATAAATAATTTAT
*
1290121 GTATCAAAAAATATATAA-ATATCATAATTTA
1 GTATCAAAAAATATATAATATA-AATAATTTA
1290152 GAATAATATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 3 0.12
32 23 0.88
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (32 bp):
GTATCAAAAAATATATAATATAAATAATTTAT
Found at i:1292800 original size:21 final size:20
Alignment explanation
Indices: 1292732--1292801 Score: 60
Period size: 21 Copynumber: 3.6 Consensus size: 20
1292722 TATTAAGATT
1292732 TAAATTTTAAATTAATTAAA
1 TAAATTTTAAATTAATTAAA
*
1292752 TATAATTTTAAA--AAAT-AA
1 TA-AATTTTAAATTAATTAAA
**
1292770 T-AA-TACAAATTAATTAAA
1 TAAATTTTAAATTAATTAAA
1292788 TTAAATTTTAAATT
1 -TAAATTTTAAATT
1292802 TAAATAAACT
Statistics
Matches: 37, Mismatches: 6, Indels: 13
0.66 0.11 0.23
Matches are distributed among these distances:
15 4 0.11
16 2 0.05
17 3 0.08
18 5 0.14
19 4 0.11
20 4 0.11
21 15 0.41
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAATTTTAAATTAATTAAA
Found at i:1293622 original size:18 final size:18
Alignment explanation
Indices: 1293576--1293622 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
1293566 ATGCTTAGTA
1293576 ATAAT-TATG-ATATAAT
1 ATAATATATGAATATAAT
* * *
1293592 AAAAAATACGAATATAAT
1 ATAATATATGAATATAAT
1293610 ATAATATATGAAT
1 ATAATATATGAAT
1293623 CATCAAGTCT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
16 3 0.13
17 3 0.13
18 17 0.74
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.34
Consensus pattern (18 bp):
ATAATATATGAATATAAT
Found at i:1294477 original size:29 final size:29
Alignment explanation
Indices: 1294444--1294499 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
1294434 TATTACACTT
* *
1294444 AAATAACTTTTTAATTTTTAAGTTGTATA
1 AAATAAATCTTTAATTTTTAAGTTGTATA
*
1294473 AAATAAATCTTTAATTTTTAATTTGTA
1 AAATAAATCTTTAATTTTTAAGTTGTA
1294500 CTTAAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.52
Consensus pattern (29 bp):
AAATAAATCTTTAATTTTTAAGTTGTATA
Found at i:1294652 original size:50 final size:50
Alignment explanation
Indices: 1294595--1294696 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
1294585 GTACCAAAAA
1294595 TACAAAAGTTTACCAAAAAAATTAAAATTATTAAAAACTTTTTAATATTT
1 TACAAAAGTTTACCAAAAAAATTAAAATTATTAAAAACTTTTTAATATTT
*
1294645 TACAAAAGTTTACCTAAAAAATTAAAATTATTAAAAACTTTTTAATATTT
1 TACAAAAGTTTACCAAAAAAATTAAAATTATTAAAAACTTTTTAATATTT
1294695 TA
1 TA
1294697 TCTTTATGTA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.39
Consensus pattern (50 bp):
TACAAAAGTTTACCAAAAAAATTAAAATTATTAAAAACTTTTTAATATTT
Found at i:1294869 original size:17 final size:18
Alignment explanation
Indices: 1294835--1294870 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1294825 TATATTATTT
*
1294835 ATTTAAATATTTTTTGTA
1 ATTTAAATATTTTATGTA
1294853 ATTTAAA-ATTTTATGTA
1 ATTTAAATATTTTATGTA
1294870 A
1 A
1294871 ATGAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (18 bp):
ATTTAAATATTTTATGTA
Found at i:1294934 original size:17 final size:17
Alignment explanation
Indices: 1294912--1294972 Score: 70
Period size: 17 Copynumber: 3.5 Consensus size: 17
1294902 ATAAATTGTG
1294912 AAAATATAAAATAAATT
1 AAAATATAAAATAAATT
1294929 AAAATATAAAATAAA-T
1 AAAATATAAAATAAATT
* *
1294945 ATAATATGAAAAAATAATT
1 AAAATAT-AAAATA-AATT
*
1294964 AAAACATAA
1 AAAATATAA
1294973 TGCGACACAG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
16 7 0.19
17 20 0.54
18 4 0.11
19 6 0.16
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (17 bp):
AAAATATAAAATAAATT
Found at i:1295746 original size:23 final size:24
Alignment explanation
Indices: 1295707--1295780 Score: 75
Period size: 23 Copynumber: 3.2 Consensus size: 24
1295697 TTAAATATAC
* *
1295707 AAAAAT-AACATAA-ACACGATAT
1 AAAAATGAATATAACACACAATAT
* *
1295729 AAAAATTAAT-TAACACACAATAC
1 AAAAATGAATATAACACACAATAT
*
1295752 AAAAATGAATATAACATA-AATAT
1 AAAAATGAATATAACACACAATAT
1295775 AAAAAT
1 AAAAAT
1295781 ATAAAAAATA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
22 9 0.21
23 28 0.65
24 6 0.14
ACGTcount: A:0.65, C:0.11, G:0.03, T:0.22
Consensus pattern (24 bp):
AAAAATGAATATAACACACAATAT
Found at i:1296204 original size:22 final size:21
Alignment explanation
Indices: 1296168--1296224 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
1296158 TAATACTTTT
1296168 AATATATA-AAAAATAA-TATA
1 AATATATATAAAAATAATTA-A
1296188 AATACTATATAAAAATAATTAA
1 AATA-TATATAAAAATAATTAA
1296210 AATATAATATAAAAA
1 AATAT-ATATAAAAA
1296225 GTGAATACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.12
21 5 0.15
22 22 0.67
23 2 0.06
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
AATATATATAAAAATAATTAA
Found at i:1296812 original size:33 final size:33
Alignment explanation
Indices: 1296743--1296817 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
1296733 AAGGTGTAGT
* * **
1296743 TGGTGCCAAAGGTTCAGGAGTTGGTACCGGTTC
1 TGGTGCCCAAGGTCCAGGAGTTGGTACCGGGGC
* *
1296776 TGGTGCCCAAGGTCCAGGAGTTGGTGCTGGGGC
1 TGGTGCCCAAGGTCCAGGAGTTGGTACCGGGGC
*
1296809 TGGTTCCCA
1 TGGTGCCCA
1296818 GTGTGTTGCT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.15, C:0.21, G:0.39, T:0.25
Consensus pattern (33 bp):
TGGTGCCCAAGGTCCAGGAGTTGGTACCGGGGC
Found at i:1296858 original size:27 final size:27
Alignment explanation
Indices: 1296827--1296913 Score: 129
Period size: 27 Copynumber: 3.2 Consensus size: 27
1296817 AGTGTGTTGC
** *
1296827 TGGTGTTTTTGGCACTGAAGGTGCAGT
1 TGGTGTTGCTGGCACTGAAGGTGTAGT
*
1296854 TGGTGTTGCTGGCACTGAAGGTGTAGC
1 TGGTGTTGCTGGCACTGAAGGTGTAGT
*
1296881 TGGTGTGGCTGGCACTGAAGGTGTAGT
1 TGGTGTTGCTGGCACTGAAGGTGTAGT
1296908 TGGTGT
1 TGGTGT
1296914 CCAAGATTCC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.14, C:0.11, G:0.41, T:0.33
Consensus pattern (27 bp):
TGGTGTTGCTGGCACTGAAGGTGTAGT
Found at i:1297019 original size:33 final size:32
Alignment explanation
Indices: 1296929--1297023 Score: 118
Period size: 33 Copynumber: 2.9 Consensus size: 32
1296919 ATTCCGGAGC
* *
1296929 TGGTGCTGGGGTTGGTGACCAAGGATCAGGAAT
1 TGGTGCTGGGGCTGGTG-CCAAGGTTCAGGAAT
* *
1296962 TGGTGTTGAGGCTGGTGCCCAAGGTTCAGGAAT
1 TGGTGCTGGGGCTGGTG-CCAAGGTTCAGGAAT
*
1296995 TGGTGCTGGGGCTGCTGCCGAAGGTTCAG
1 TGGTGCTGGGGCTGGTGCC-AAGGTTCAG
1297024 TTCGTGTTGG
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
32 2 0.04
33 51 0.96
ACGTcount: A:0.17, C:0.16, G:0.42, T:0.25
Consensus pattern (32 bp):
TGGTGCTGGGGCTGGTGCCAAGGTTCAGGAAT
Found at i:1298944 original size:20 final size:21
Alignment explanation
Indices: 1298891--1298944 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 21
1298881 AATTTTTAGT
1298891 TAAA-TTTAATTATAAAATATA
1 TAAATTTTAA-TATAAAATATA
*
1298912 TAAATTTTGATATAAAA-ATA
1 TAAATTTTAATATAAAATATA
1298932 -AATATTTTAATAT
1 TAA-ATTTTAATAT
1298945 TTTAAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 2 0.07
20 12 0.41
21 11 0.38
22 4 0.14
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TAAATTTTAATATAAAATATA
Found at i:1299837 original size:23 final size:21
Alignment explanation
Indices: 1299802--1299847 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
1299792 CATAATATTT
* *
1299802 TATTTAAATTTAATTATAAAATA
1 TATTAAAAATTAA-TAT-AAATA
1299825 TATTAAAAATTAATATAAATA
1 TATTAAAAATTAATATAAATA
1299846 TA
1 TA
1299848 ATAATTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 3 0.14
23 11 0.52
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TATTAAAAATTAATATAAATA
Found at i:1300077 original size:2 final size:2
Alignment explanation
Indices: 1300070--1300102 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1300060 TTCTGATTTA
1300070 AT 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 AT A
1300103 AAGAAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1305435 original size:11 final size:11
Alignment explanation
Indices: 1305419--1305447 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
1305409 AATTTATAAT
1305419 TTATAATTAAA
1 TTATAATTAAA
1305430 TTATAA-TAAA
1 TTATAATTAAA
1305440 TTATAATT
1 TTATAATT
1305448 TTATAGATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TTATAATTAAA
Found at i:1305443 original size:21 final size:19
Alignment explanation
Indices: 1305407--1305447 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
1305397 GTAATTGAAA
*
1305407 TAAATTTATAATTTATAAT
1 TAAATTTATAAATTATAAT
1305426 TAAATTATAATAAATTATAAT
1 TAAATT-T-ATAAATTATAAT
1305447 T
1 T
1305448 TTATAGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 1 0.05
21 12 0.63
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TAAATTTATAAATTATAAT
Found at i:1305909 original size:15 final size:15
Alignment explanation
Indices: 1305891--1305920 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1305881 AGTATAAAAA
*
1305891 ATTTTCAATTTTTTT
1 ATTTTAAATTTTTTT
1305906 ATTTTAAATTTTTTT
1 ATTTTAAATTTTTTT
1305921 TTATTTTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (15 bp):
ATTTTAAATTTTTTT
Found at i:1305929 original size:19 final size:18
Alignment explanation
Indices: 1305899--1305938 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
1305889 AAATTTTCAA
1305899 TTTTTTTATTTTAAAT-T
1 TTTTTTTATTTTAAATAT
1305916 TTTTTTTATTTTTTAAATAT
1 TTTTTTTA--TTTTAAATAT
1305936 TTT
1 TTT
1305939 CTTCCATGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.40
19 8 0.40
20 4 0.20
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTTTATTTTAAATAT
Found at i:1309420 original size:2 final size:2
Alignment explanation
Indices: 1309415--1309443 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1309405 TTATATTTTC
1309415 TA TA 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 TA TA T
1309444 TACTCTATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1311325 original size:114 final size:113
Alignment explanation
Indices: 1311129--1311335 Score: 265
Period size: 114 Copynumber: 1.8 Consensus size: 113
1311119 TTATCATGGG
* * * *
1311129 CATTATTAGTCAATTTTATGACAATGATTAAAATCATTCCACCATCCAAATAGGTTTAAAAGTAT
1 CATTATTAGTCAATTTTATGACAATAATGAAAATCATTCCACCATCCAAATAGGTCTAAAAGCAT
*
1311194 TAATCTTGCTATTTTAAATGTTTTCATACTCAAATTTTTTTTTATGAA
66 TAATCTTGCTATTTTAAATATTTTCATACTCAAATTTTTTTTTATGAA
* * * *
1311242 CATTATTAGTCATTTTTATGACCATAATGAAAA-CTATGTCTACCA-CTCAAATAGGTCTAATAG
1 CATTATTAGTCAATTTTATGACAATAATGAAAATC-AT-TCCACCATC-CAAATAGGTCTAAAAG
* * *
1311305 CATTCATTTTGCTCTTTTAAATATTTTCATA
63 CATTAATCTTGCTATTTTAAATATTTTCATA
1311336 TTCATAAGAC
Statistics
Matches: 79, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
112 1 0.01
113 32 0.41
114 46 0.58
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43
Consensus pattern (113 bp):
CATTATTAGTCAATTTTATGACAATAATGAAAATCATTCCACCATCCAAATAGGTCTAAAAGCAT
TAATCTTGCTATTTTAAATATTTTCATACTCAAATTTTTTTTTATGAA
Found at i:1313052 original size:21 final size:20
Alignment explanation
Indices: 1313010--1313053 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
1313000 AATAATAGCA
1313010 TAAATTAATTAAATTAAATT
1 TAAATTAATTAAATTAAATT
*
1313030 TAAATTTATTACAA-TATAATT
1 TAAATTAATTA-AATTA-AATT
1313051 TAA
1 TAA
1313054 TATCATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAATTAATTAAATTAAATT
Found at i:1314078 original size:2 final size:2
Alignment explanation
Indices: 1314071--1314099 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1314061 TAAAGAGAAT
1314071 TA TA 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 TA TA T
1314100 TTTAAATGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1315877 original size:2 final size:2
Alignment explanation
Indices: 1315870--1315906 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1315860 GCCTTTACAA
1315870 AT AT AT 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 AT AT AT A
1315907 AAGAATTCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1317888 original size:191 final size:192
Alignment explanation
Indices: 1317564--1317946 Score: 579
Period size: 191 Copynumber: 2.0 Consensus size: 192
1317554 ATTAAATAAT
* * *
1317564 ACATAAAATCTTTTAATATATCTATAAAATCTTTTCTAAACTTATCAGCTTTTTAACTTGGACAA
1 ACATAAAATCTTTTAATATATCTATAAAATCTTTTCTAAACTCATCAGCATTTTAACTTAGACAA
* * *
1317629 ATAAGCTGAGTACAAAGAATGGAGAAAAAGCAATAAAAATGAATACACGACAACCAAAGGAAAAA
66 ATAAGCTGAGTACAAAGAATGAAAAAAAAGCAATAAAAATGAATACACGAAAACCAAAGGAAAAA
* * *
1317694 TGAAAAAAATAATAGCTGACACATGAATAAGCTCAGCTTTCAGGGA-TTATCTAAAATTTAA
131 TGAAAAAAATAATAGCTGACACATGAATAAGCTCAACTTTCAAGGATTTATCCAAAATTTAA
* * * *
1317755 ACATAAAATCTTTTAATATCTCTGTAAAATCTTTTCTAAGCTCATCAGCATTTTAACTTAGTCAA
1 ACATAAAATCTTTTAATATATCTATAAAATCTTTTCTAAACTCATCAGCATTTTAACTTAGACAA
* * * *
1317820 ATAGGCTGAGTACAAAGAATGAAAAAAAAGCAATAGAAATGACTACACGAAAATCAAAGGAAAAA
66 ATAAGCTGAGTACAAAGAATGAAAAAAAAGCAATAAAAATGAATACACGAAAACCAAAGGAAAAA
* * *
1317885 TGAAAAAAATAATAGCTGACACGTGGATAAGCTCAACTTTCAAGGATTTGTCCAAAATTTAA
131 TGAAAAAAATAATAGCTGACACATGAATAAGCTCAACTTTCAAGGATTTATCCAAAATTTAA
1317947 GATTTAATTA
Statistics
Matches: 171, Mismatches: 20, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
191 158 0.92
192 13 0.08
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.27
Consensus pattern (192 bp):
ACATAAAATCTTTTAATATATCTATAAAATCTTTTCTAAACTCATCAGCATTTTAACTTAGACAA
ATAAGCTGAGTACAAAGAATGAAAAAAAAGCAATAAAAATGAATACACGAAAACCAAAGGAAAAA
TGAAAAAAATAATAGCTGACACATGAATAAGCTCAACTTTCAAGGATTTATCCAAAATTTAA
Found at i:1321053 original size:26 final size:26
Alignment explanation
Indices: 1321001--1321059 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
1320991 AAGATATAAG
*
1321001 AATAATTAATAAATTATGAATTTTTT
1 AATAATTAATAAATTATGAATTATTT
* *
1321027 AATATTTAA-AAATTATTAATATATTT
1 AATAATTAATAAATTATGAAT-TATTT
1321053 AATAATT
1 AATAATT
1321060 CGTATATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 10 0.36
26 18 0.64
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (26 bp):
AATAATTAATAAATTATGAATTATTT
Found at i:1321117 original size:16 final size:17
Alignment explanation
Indices: 1321096--1321128 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1321086 TGTCATATTT
1321096 TATTTA-AAAAATTTTA
1 TATTTATAAAAATTTTA
*
1321112 TATTTATATAAATTTTA
1 TATTTATAAAAATTTTA
1321129 ATAAAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATTTATAAAAATTTTA
Found at i:1321151 original size:32 final size:31
Alignment explanation
Indices: 1321092--1321152 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
1321082 ATTATGTCAT
* *
1321092 ATTTTATTTAAAAAATTTTATATTTATATAA
1 ATTTTAATAAAAAAATTTTATATTTATATAA
1321123 ATTTTAATAAAAAAATAATTTATA-TTATAT
1 ATTTTAATAAAAAAAT--TTTATATTTATAT
1321153 TTTTTAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 14 0.54
32 6 0.23
33 6 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
ATTTTAATAAAAAAATTTTATATTTATATAA
Found at i:1321161 original size:25 final size:25
Alignment explanation
Indices: 1321134--1321180 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1321124 TTTTAATAAA
1321134 AAAATA-ATTTATATTATATTTTTT
1 AAAATATATTTATATTATATTTTTT
* *
1321158 AAAATATATTTTTATTTTATTTT
1 AAAATATATTTATATTATATTTT
1321181 AATTATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
AAAATATATTTATATTATATTTTTT
Found at i:1321437 original size:31 final size:32
Alignment explanation
Indices: 1321396--1321472 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 32
1321386 ATAATATTAA
* *
1321396 TATAATATAAATATAAAT-ATATGTTAAAATT
1 TATAAAATAAATATAAATAATATATTAAAATT
* * * *
1321427 TATAAAATAAAAATTATTAATATATTAAATTT
1 TATAAAATAAATATAAATAATATATTAAAATT
1321459 TATATAAATAAATA
1 TATA-AAATAAATA
1321473 ATTTTTTATA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
31 14 0.38
32 15 0.41
33 8 0.22
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (32 bp):
TATAAAATAAATATAAATAATATATTAAAATT
Found at i:1321492 original size:19 final size:19
Alignment explanation
Indices: 1321440--1321493 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 19
1321430 AAAATAAAAA
1321440 TTAT-TAATATATTA-AATT
1 TTATATAATA-ATTATAATT
1321458 TTATATAAATAA--ATAATT
1 TTATAT-AATAATTATAATT
*
1321476 TTTTATAATAATTATAAT
1 TTATATAATAATTATAAT
1321494 ATAAAAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
17 6 0.20
18 13 0.43
19 7 0.23
20 4 0.13
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTATATAATAATTATAATT
Found at i:1321502 original size:17 final size:15
Alignment explanation
Indices: 1321482--1321525 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 15
1321472 AATTTTTTAT
1321482 AATAATTATAATATAAA
1 AATAA-TATAA-ATAAA
*
1321499 AATAATATAAATATA
1 AATAATATAAATAAA
1321514 AATAATATAAAT
1 AATAATATAAAT
1321526 TATTAAATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 16 0.62
16 5 0.19
17 5 0.19
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AATAATATAAATAAA
Found at i:1321921 original size:18 final size:18
Alignment explanation
Indices: 1321889--1321940 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 18
1321879 TTAAATTTAA
1321889 TTATAAAATATATAAATATT
1 TTATAAAA-A-ATAAATATT
1321909 ATTAT-AAAAAT-AATATT
1 -TTATAAAAAATAAATATT
*
1321926 TTTTAAAAAATAAAT
1 TTATAAAAAATAAAT
1321941 TGAGCTAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 3 0.11
17 12 0.43
18 5 0.18
19 1 0.04
20 3 0.11
21 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TTATAAAAAATAAATATT
Found at i:1325864 original size:16 final size:16
Alignment explanation
Indices: 1325826--1325880 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 16
1325816 CTCAAATTTT
1325826 ATATAAATATATTATA
1 ATATAAATATATTATA
* * *
1325842 TTTTAAATATTTTATA
1 ATATAAATATATTATA
1325858 ATATAAA-A-A--ATA
1 ATATAAATATATTATA
1325870 ATATAAATATA
1 ATATAAATATA
1325881 AAATAAATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
12 10 0.32
13 1 0.03
14 1 0.03
15 1 0.03
16 18 0.58
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATATAAATATATTATA
Found at i:1325883 original size:17 final size:18
Alignment explanation
Indices: 1325857--1325893 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
1325847 AATATTTTAT
1325857 AATATAAAAA-ATAATATA
1 AATATAAAAATA-AATATA
1325875 AATAT-AAAATAAATATA
1 AATATAAAAATAAATATA
1325892 AA
1 AA
1325894 AATTATGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
AATATAAAAATAAATATA
Found at i:1326474 original size:22 final size:22
Alignment explanation
Indices: 1326439--1326501 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
1326429 ATGAATTATT
**
1326439 AATATATTTTATATAAATATAA
1 AATATATTAAATATAAATATAA
*
1326461 AATATATTAAATAT-GATCATAA
1 AATATATTAAATATAAAT-ATAA
*
1326483 AATA-ATAAAATATAAATAT
1 AATATATTAAATATAAATAT
1326502 GACATAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
21 12 0.35
22 22 0.65
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
AATATATTAAATATAAATATAA
Found at i:1326498 original size:27 final size:27
Alignment explanation
Indices: 1326451--1326527 Score: 86
Period size: 27 Copynumber: 2.8 Consensus size: 27
1326441 TATATTTTAT
*
1326451 ATAAATATAAAATATATTAAATATGATC
1 ATAAATATAAAAAATATTAAATATGA-C
1326479 ATAAA-ATAATAAAATA-TAAATATGAC
1 ATAAATATAA-AAAATATTAAATATGAC
*
1326505 ATAAATTATCAAAAATACTTAAA
1 ATAAA-TATAAAAAATA-TTAAA
1326528 CATTATAGCG
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
26 6 0.14
27 19 0.45
28 13 0.31
29 4 0.10
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.31
Consensus pattern (27 bp):
ATAAATATAAAAAATATTAAATATGAC
Found at i:1329040 original size:2 final size:2
Alignment explanation
Indices: 1329033--1329057 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1329023 TATTTTCTTT
1329033 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
1329058 TACTCTATAG
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:1329552 original size:24 final size:24
Alignment explanation
Indices: 1329524--1329587 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
1329514 TTTATCAAAG
* *
1329524 AAAAATATATTTAAATTTTATTAT
1 AAAAATATATTTAAATATTAATAT
* *
1329548 AAAAAGATATATAAATATTAATAT
1 AAAAATATATTTAAATATTAATAT
1329572 AAAAGATAATATTTAA
1 AAAA-AT-ATATTTAA
1329588 TGTATTTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
24 24 0.75
25 1 0.03
26 7 0.22
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (24 bp):
AAAAATATATTTAAATATTAATAT
Found at i:1332150 original size:8 final size:9
Alignment explanation
Indices: 1332132--1332177 Score: 53
Period size: 8 Copynumber: 5.2 Consensus size: 9
1332122 TTAAAAATTA
1332132 TTAATATAT
1 TTAATATAT
1332141 TTAATA-AT
1 TTAATATAT
1332149 TT-ATATAT
1 TTAATATAT
1332157 TTATATTATAT
1 TTA-A-TATAT
1332168 TT-ATATAT
1 TTAATATAT
1332176 TT
1 TT
1332178 TATTATATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
7 3 0.09
8 15 0.45
9 7 0.21
10 1 0.03
11 7 0.21
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
TTAATATAT
Found at i:1332192 original size:23 final size:19
Alignment explanation
Indices: 1332130--1332185 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 19
1332120 ATTTAAAAAT
*
1332130 TATTAATATATTTA-A-TA
1 TATTTATATATTTATATTA
1332147 -ATTTATATATTTATATTA
1 TATTTATATATTTATATTA
1332165 TATTTATATATTT-TATTA
1 TATTTATATATTTATATTA
1332183 TAT
1 TAT
1332186 CATATTTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
16 12 0.34
17 1 0.03
18 10 0.29
19 12 0.34
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TATTTATATATTTATATTA
Found at i:1332214 original size:16 final size:17
Alignment explanation
Indices: 1332193--1332225 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1332183 TATCATATTT
1332193 TATTTA-AAAAATTTTA
1 TATTTATAAAAATTTTA
*
1332209 TATTTATATAAATTTTA
1 TATTTATAAAAATTTTA
1332226 ATATAGATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATTTATAAAAATTTTA
Found at i:1332501 original size:11 final size:11
Alignment explanation
Indices: 1332485--1332607 Score: 52
Period size: 10 Copynumber: 12.0 Consensus size: 11
1332475 AAAATAAAAA
*
1332485 ATAATATTAAT
1 ATAATATAAAT
1332496 ATAATATAAAT
1 ATAATATAAAT
1332507 AT-A-A-AAAT
1 ATAATATAAAT
*
1332515 ATATTA-AAAT
1 ATAATATAAAT
*
1332525 -TTATATAAAT
1 ATAATATAAAT
**
1332535 AT-ATA-ATTT
1 ATAATATAAAT
* *
1332544 TTAAAAT-AAT
1 ATAATATAAAT
*
1332554 -TAATATAAAAA
1 ATAATAT-AAAT
1332565 ATAATATAAAT
1 ATAATATAAAT
*
1332576 ACAA-ATAAAT
1 ATAATATAAAT
*
1332586 ATATTATTAAAT
1 ATAATA-TAAAT
*
1332598 TTAATA-AAAT
1 ATAATATAAAT
1332608 CTTAAAACTT
Statistics
Matches: 83, Mismatches: 18, Indels: 23
0.67 0.15 0.19
Matches are distributed among these distances:
8 6 0.07
9 12 0.14
10 28 0.34
11 22 0.27
12 15 0.18
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:1332518 original size:16 final size:16
Alignment explanation
Indices: 1332499--1332576 Score: 50
Period size: 16 Copynumber: 4.6 Consensus size: 16
1332489 TATTAATATA
1332499 ATATAAATATAAAAAT
1 ATATAAATATAAAAAT
*
1332515 ATATTAAAATTTATATAAAT
1 ATA-T-AAA--TATAAAAAT
* * *
1332535 ATATAATTTTTAAAAT
1 ATATAAATATAAAAAT
*
1332551 A-ATTAATATAAAAAAT
1 ATATAAATAT-AAAAAT
1332567 AATATAAATA
1 -ATATAAATA
1332577 CAAATAAATA
Statistics
Matches: 45, Mismatches: 10, Indels: 12
0.67 0.15 0.18
Matches are distributed among these distances:
15 5 0.11
16 15 0.33
17 2 0.04
18 11 0.24
19 1 0.02
20 11 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATAAATATAAAAAT
Found at i:1332530 original size:28 final size:28
Alignment explanation
Indices: 1332460--1332564 Score: 91
Period size: 27 Copynumber: 4.0 Consensus size: 28
1332450 AATTAAAAGT
* *
1332460 TATA-TAAAATTGATAAAAATA-AAAAA
1 TATATTAAAATTAATATAAATATAAAAA
*
1332486 TAATATTAATA-TAATATAAATATAAAAA
1 T-ATATTAAAATTAATATAAATATAAAAA
* *
1332514 TATATTAAAATTTATATAAATAT-ATAA
1 TATATTAAAATTAATATAAATATAAAAA
*
1332541 T-TTTTAAAA-TAAT-T-AATATAAAAA
1 TATATTAAAATTAATATAAATATAAAAA
1332565 ATAATATAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
23 5 0.08
24 4 0.06
25 3 0.05
26 8 0.12
27 24 0.37
28 21 0.32
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (28 bp):
TATATTAAAATTAATATAAATATAAAAA
Found at i:1333000 original size:17 final size:17
Alignment explanation
Indices: 1332950--1333000 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
1332940 TTTAAATTTA
1332950 ATTA-TAAAATATATAAAT
1 ATTATTAAAATA-AT-AAT
1332968 ATTATTATAAA-AATAAT
1 ATTATTA-AAATAATAAT
*
1332985 ATTTTTAAAATAATAA
1 ATTATTAAAATAATAA
1333001 ATTGAGCTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 3 0.10
17 14 0.48
18 6 0.21
19 3 0.10
20 3 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTATTAAAATAATAAT
Found at i:1334005 original size:50 final size:50
Alignment explanation
Indices: 1333930--1334089 Score: 212
Period size: 50 Copynumber: 3.2 Consensus size: 50
1333920 CTATCAAAAT
* * * * *
1333930 TAATTGTTAATTATTTTTTATCAACCTTTGACAATCGAGAGAGATGGTCG
1 TAATTGTTGATTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCG
* * *
1333980 TAATTGTTGATTATTCTTCACCAACCTTTGATAATCAAGAGAGGTGATCG
1 TAATTGTTGATTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCG
* * *
1334030 TAATTGTTGATTATTCTTCACCAACCTTTGACAATAGACAGAGGTGGCCG
1 TAATTGTTGATTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCG
*
1334080 TTATTGTTGA
1 TAATTGTTGA
1334090 CTCTAAGAAA
Statistics
Matches: 95, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 95 1.00
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.38
Consensus pattern (50 bp):
TAATTGTTGATTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCG
Found at i:1338081 original size:20 final size:20
Alignment explanation
Indices: 1338034--1338108 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
1338024 AAAAAGACAT
*
1338034 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
1338053 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
1338074 CATGTATCGATATATTAAAA
1 AATGTATCGATACATTCATA
1338094 AATGTATCGATACAT
1 AATGTATCGATACAT
1338109 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:1338102 original size:40 final size:39
Alignment explanation
Indices: 1338031--1338108 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
1338021 GGTAAAAAGA
** *
1338031 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTAAAAAATATATCGATACATT
* *
1338070 CATACATGTATCGATATATTAAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTAAAAAATATATCGATACAT
1338109 CAGGGTATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTAAAAAATATATCGATACATT
Done.