Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1474
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: 108252
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1702 original size:27 final size:27
Alignment explanation
Indices: 1667--1867 Score: 235
Period size: 27 Copynumber: 7.4 Consensus size: 27
1657 TAAATTGTAC
1667 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
1694 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
1721 TGCA-TAAGTGTGGCGAAATGAATATG-
1 AGCACTAAGTGT-GCGATTTGACTATGT
* * *
1747 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
1775 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
1803 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
1830 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
1857 AGCACTGAGTG
1 AGCACTAAGTG
1868 AGCGGACTCA
Statistics
Matches: 150, Mismatches: 19, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
26 7 0.05
27 113 0.75
28 30 0.20
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:13379 original size:26 final size:26
Alignment explanation
Indices: 13342--13447 Score: 176
Period size: 26 Copynumber: 4.1 Consensus size: 26
13332 GTACAAATTA
13342 ATAATGGGTTAGGTAAATGTTCCATG
1 ATAATGGGTTAGGTAAATGTTCCATG
* *
13368 ATAATGGATTAGGTAAATATTCCATG
1 ATAATGGGTTAGGTAAATGTTCCATG
13394 ATAATGGGTTAGGTAAATGTTCCATG
1 ATAATGGGTTAGGTAAATGTTCCATG
* *
13420 ATAATAGTTTAGGTAAATGTTCCATG
1 ATAATGGGTTAGGTAAATGTTCCATG
13446 AT
1 AT
13448 GGGCATTTCA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
26 74 1.00
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.36
Consensus pattern (26 bp):
ATAATGGGTTAGGTAAATGTTCCATG
Found at i:29595 original size:43 final size:42
Alignment explanation
Indices: 29522--29602 Score: 117
Period size: 43 Copynumber: 1.9 Consensus size: 42
29512 TCTGCGACAT
** *
29522 GGCTTTGGCATCGATATGTAATTTCGTGTAAGACCATAGCTG
1 GGCTTTGGCATCGATATGTAATCCCATGTAAGACCATAGCTG
*
29564 GGCTATTGGCATCGATATGTGATCCCATGTAAGACCATA
1 GGCT-TTGGCATCGATATGTAATCCCATGTAAGACCATA
29603 TCCGAGATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
42 4 0.12
43 30 0.88
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.31
Consensus pattern (42 bp):
GGCTTTGGCATCGATATGTAATCCCATGTAAGACCATAGCTG
Found at i:34223 original size:40 final size:41
Alignment explanation
Indices: 34138--34231 Score: 113
Period size: 40 Copynumber: 2.3 Consensus size: 41
34128 CTAAGTTCGA
34138 CACTAAGTGTGCG-GTTCAAAATAGCTTCGGCTACAAATGG
1 CACTAAGTGTGCGAGTTCAAAATAGCTTCGGCTACAAATGG
* ** * *
34178 TACTAAGTGTGCGAGTT-GGAATAGCTTCGGCTATATGA-GG
1 CACTAAGTGTGCGAGTTCAAAATAGCTTCGGCTACA-AATGG
34218 CACTAAGTGTGCGA
1 CACTAAGTGTGCGA
34232 TACCAAGATA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
40 42 0.91
41 4 0.09
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.27
Consensus pattern (41 bp):
CACTAAGTGTGCGAGTTCAAAATAGCTTCGGCTACAAATGG
Found at i:38872 original size:20 final size:20
Alignment explanation
Indices: 38838--38886 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
38828 ATCTCGTTTT
*
38838 CAAATCATATAATCAACATCA
1 CAAATCATATAATCAA-AACA
*
38859 CAAA-CATATCATCAAAACA
1 CAAATCATATAATCAAAACA
38878 CAAATCATA
1 CAAATCATA
38887 CCTATCATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 7 0.28
20 14 0.56
21 4 0.16
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.20
Consensus pattern (20 bp):
CAAATCATATAATCAAAACA
Found at i:41025 original size:43 final size:43
Alignment explanation
Indices: 40964--41059 Score: 149
Period size: 43 Copynumber: 2.2 Consensus size: 43
40954 ACTTAGTTCT
40964 AATTAATTAACCGAAGCTATAATTGTATTGCACACCTAGTGCC
1 AATTAATTAACCGAAGCTATAATTGTATTGCACACCTAGTGCC
* * *
41007 AATTAATTAGCTGAAGCTATAATTGTATTGCACACTTAGTGCC
1 AATTAATTAACCGAAGCTATAATTGTATTGCACACCTAGTGCC
41050 -ATTATATTAA
1 AATTA-ATTAA
41060 ATCGAACTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 4 0.08
43 44 0.92
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (43 bp):
AATTAATTAACCGAAGCTATAATTGTATTGCACACCTAGTGCC
Found at i:43041 original size:43 final size:43
Alignment explanation
Indices: 42985--43153 Score: 184
Period size: 43 Copynumber: 4.0 Consensus size: 43
42975 ATATCGTACA
** *
42985 ATGCCAACATCCCAGACGTGGTCTTACATGAAATCACATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGAAATCACATATCG
* *
43028 ATGCCACTGTCCCAGACAG-GGTCTTACACG-AATCAAATA-CG
1 ATGCCAATGTCCCAGAC-GTGGTCTTACACGAAATCACATATCG
* * * *
43069 ATGCCAATGTTCTAGACATGGTCTTACACGTAATCACATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGAAATCACATATCG
* * *
43112 ATTCCAATATCCCAGACGTGGTCTTACATGAGAA-CACATATC
1 ATGCCAATGTCCCAGACGTGGTCTTACACGA-AATCACATATC
43154 AAAAATCCTA
Statistics
Matches: 104, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
41 27 0.26
42 16 0.15
43 58 0.56
44 3 0.03
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.25
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACGTGGTCTTACACGAAATCACATATCG
Found at i:44304 original size:14 final size:15
Alignment explanation
Indices: 44287--44315 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
44277 ATACAAAAAT
44287 TTCACACAT-ATAAA
1 TTCACACATAATAAA
44301 TTCACACATAATAAA
1 TTCACACATAATAAA
44316 CATAGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:49233 original size:28 final size:28
Alignment explanation
Indices: 49170--49295 Score: 236
Period size: 28 Copynumber: 4.5 Consensus size: 28
49160 ATATTAAGTC
*
49170 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
49197 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
49225 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
49253 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
49281 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
49296 GTACAATTTA
Statistics
Matches: 97, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
27 22 0.23
28 75 0.77
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:57245 original size:28 final size:28
Alignment explanation
Indices: 57182--57307 Score: 227
Period size: 28 Copynumber: 4.5 Consensus size: 28
57172 ATATTAAGTC
*
57182 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
57209 CGCACACTTAGTGATATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
57237 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
57265 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
57293 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
57308 GTACAATTTA
Statistics
Matches: 95, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
27 21 0.22
28 74 0.78
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:62768 original size:17 final size:17
Alignment explanation
Indices: 62746--62801 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
62736 GCCCATTTAA
62746 TTTTCAATTTTTTTTTC
1 TTTTCAATTTTTTTTTC
**
62763 TTTTC-ATTTTCATTTC
1 TTTTCAATTTTTTTTTC
*
62779 ATTTTCATTTTATTTTTGTC
1 -TTTTCAATTT-TTTTT-TC
62799 TTT
1 TTT
62802 ATTTATCATT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
16 9 0.30
17 10 0.33
18 3 0.10
19 6 0.20
20 2 0.07
ACGTcount: A:0.12, C:0.12, G:0.02, T:0.73
Consensus pattern (17 bp):
TTTTCAATTTTTTTTTC
Found at i:62772 original size:6 final size:6
Alignment explanation
Indices: 62745--62794 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 6
62735 AGCCCATTTA
*
62745 ATTTTC AATTTT- TTTTTC -TTTTC ATTTTC A-TTTC ATTTTC ATTTT-
1 ATTTTC -ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC
62790 ATTTT
1 ATTTT
62795 TGTCTTTATT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 19 0.49
6 15 0.38
7 5 0.13
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (6 bp):
ATTTTC
Found at i:66479 original size:42 final size:42
Alignment explanation
Indices: 66432--66515 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
66422 GATTACCAAA
*
66432 AGGATAGGGTCGGTAGCATATTGATTGGCTTTACCGTCTGAG
1 AGGATAGGGTCGATAGCATATTGATTGGCTTTACCGTCTGAG
66474 AGGATAGGGTCGATAGCATATTGATTGGCTTTACCGTCTGAG
1 AGGATAGGGTCGATAGCATATTGATTGGCTTTACCGTCTGAG
66516 TTGGAAAGAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.23, C:0.14, G:0.32, T:0.31
Consensus pattern (42 bp):
AGGATAGGGTCGATAGCATATTGATTGGCTTTACCGTCTGAG
Found at i:71874 original size:50 final size:50
Alignment explanation
Indices: 71799--72010 Score: 343
Period size: 50 Copynumber: 4.2 Consensus size: 50
71789 CACTCATTTA
* *
71799 GCCGAATACACAAGATCAAATATAACATCACATTTGTACATACCTATATG
1 GCCGAATATACAAGATCAAATATAACATCACATATGTACATACCTATATG
*
71849 GCCGAATATACAAGATCAAATATAACATCACATATGTACATACCTATGTG
1 GCCGAATATACAAGATCAAATATAACATCACATATGTACATACCTATATG
* * * *
71899 GCCGAATATACAACATCAAATATAACATCACATATCTACATACCAATAGG
1 GCCGAATATACAAGATCAAATATAACATCACATATGTACATACCTATATG
* *
71949 GTCGAATATACAAGATCAAATATAACATCACATATGTACATACCTATCTG
1 GCCGAATATACAAGATCAAATATAACATCACATATGTACATACCTATATG
71999 GCCGAATATACA
1 GCCGAATATACA
72011 TGGTCATTTA
Statistics
Matches: 147, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 147 1.00
ACGTcount: A:0.43, C:0.22, G:0.10, T:0.25
Consensus pattern (50 bp):
GCCGAATATACAAGATCAAATATAACATCACATATGTACATACCTATATG
Found at i:74420 original size:36 final size:36
Alignment explanation
Indices: 74366--74437 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
74356 ACCGCGATGT
*
74366 AAATCTCAGATCTGTATCTGACACAATAGAAATAGG
1 AAATCTCAGATCTCTATCTGACACAATAGAAATAGG
74402 AAATCTC-GAATCTCTATCTGACACAATAGAAATAGG
1 AAATCTCAG-ATCTCTATCTGACACAATAGAAATAGG
74438 TACTCCGTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 1 0.03
36 33 0.97
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.25
Consensus pattern (36 bp):
AAATCTCAGATCTCTATCTGACACAATAGAAATAGG
Found at i:79468 original size:50 final size:50
Alignment explanation
Indices: 79409--79666 Score: 408
Period size: 50 Copynumber: 5.2 Consensus size: 50
79399 CATTTAGTCA
* * *
79409 AATACACAAGATCCAATATAACATCACATATGTACATACCTATATGGCCG
1 AATATACAAGATCAAATATAACATCACATATGTACATACCTATGTGGCCG
79459 AATATACAAGATCAAATATAACATCACATATGTACATACCTATGTGGCCG
1 AATATACAAGATCAAATATAACATCACATATGTACATACCTATGTGGCCG
* ***
79509 AATATACACGATCAAATATAACATCACATATGTACATACCTATGTTATCG
1 AATATACAAGATCAAATATAACATCACATATGTACATACCTATGTGGCCG
* * *
79559 AATATACAAGTTCAAATATATCATCACATATCTACATACCTATGTGGCCG
1 AATATACAAGATCAAATATAACATCACATATGTACATACCTATGTGGCCG
* *
79609 AATATACAAGATCAAATATAACATCACATATGTACATGCCTATGTGGCTG
1 AATATACAAGATCAAATATAACATCACATATGTACATACCTATGTGGCCG
79659 AATATACA
1 AATATACA
79667 TGGTCATTTA
Statistics
Matches: 189, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 189 1.00
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (50 bp):
AATATACAAGATCAAATATAACATCACATATGTACATACCTATGTGGCCG
Found at i:95204 original size:96 final size:95
Alignment explanation
Indices: 95011--95390 Score: 593
Period size: 96 Copynumber: 4.0 Consensus size: 95
95001 CCCTTCGGGA
* * * * * *
95011 CTTATCAC-ATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACA
1 CTTATCACAATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACA
*
95075 CTTTCACATTCATCACATCGACCATTAGGC
66 CTTTCACATTCATCACATCGGCCATTAGGC
* * *
95105 CTTATCAC-ATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATATA
1 CTTATCACAATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATATA
95169 CACTTTCACATTCATCACATCGGCCATTAGGC
64 CACTTTCACATTCATCACATCGGCCATTAGGC
95201 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 CTTATCACA-ATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
95266 ACTTTCACATTCATCACATCGGCCATTAGGC
65 ACTTTCACATTCATCACATCGGCCATTAGGC
95297 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAT
1 CTTATCACA-ATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATAT
*
95362 ACACTTTCACATTCATCACATTGGCCATT
63 ACACTTTCACATTCATCACATCGGCCATT
95391 CAATACCAGA
Statistics
Matches: 266, Mismatches: 14, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
94 46 0.17
96 142 0.53
98 78 0.29
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (95 bp):
CTTATCACAATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACA
CTTTCACATTCATCACATCGGCCATTAGGC
Found at i:95283 original size:145 final size:145
Alignment explanation
Indices: 95011--95391 Score: 635
Period size: 145 Copynumber: 2.7 Consensus size: 145
95001 CCCTTCGGGA
* * * * *
95011 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCAC--ATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAT
* * *
95072 ACACTTTCACATTCATCACATCGACCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
66 ACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCA
*
95137 CATCGGCTATTAGGC
131 CATCGGCCATTAGGC
* *
95152 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAT
95217 ACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCA
66 ACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCA
95282 CATCGGCCATTAGGC
131 CATCGGCCATTAGGC
95297 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAT
95362 ACACTTTCACATTCATCACATTGGCCATTC
66 ACACTTTCACATTCATCACATTGGCCATTC
95392 AATACCAGAT
Statistics
Matches: 223, Mismatches: 13, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
141 10 0.04
142 1 0.00
143 37 0.17
145 175 0.78
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (145 bp):
CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAT
ACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCA
CATCGGCCATTAGGC
Found at i:95391 original size:49 final size:49
Alignment explanation
Indices: 95011--95390 Score: 578
Period size: 49 Copynumber: 7.9 Consensus size: 49
95001 CCCTTCGGGA
* * * * *
95011 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
95058 CCTGTCAC--ATATATACACTTTCACATTCATCACATCGACCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
95105 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
95152 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
95201 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
95250 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
95297 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
95346 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATT
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATT
95391 CAATACCAGA
Statistics
Matches: 308, Mismatches: 19, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
46 1 0.00
47 132 0.43
49 175 0.57
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:100332 original size:47 final size:47
Alignment explanation
Indices: 100266--100740 Score: 817
Period size: 47 Copynumber: 10.1 Consensus size: 47
100256 GAAATGATAG
*
100266 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
100313 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
100360 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
100407 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
100454 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
100501 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
100548 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
100597 T-AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
100643 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * *
100690 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
100737 TAAG
1 TAAG
100741 TCCCGAAGGG
Statistics
Matches: 412, Mismatches: 13, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
46 12 0.03
47 354 0.86
48 34 0.08
49 12 0.03
ACGTcount: A:0.32, C:0.10, G:0.30, T:0.28
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:100915 original size:37 final size:37
Alignment explanation
Indices: 100859--100937 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
100849 CCGAGCTCTA
* * *
100859 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
100896 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
100933 AAGAC
1 AAGAC
100938 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:102831 original size:43 final size:43
Alignment explanation
Indices: 102783--102885 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
102773 TTGGTTTTCA
102783 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
102826 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
102869 GCACTAAGTGTGCGGGC
1 GCACTAAGTGTGCGGGC
102886 TTGAAATGCA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.22, C:0.16, G:0.36, T:0.26
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
Found at i:102902 original size:29 final size:29
Alignment explanation
Indices: 102867--102940 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
102857 GTTGTGAGAT
* *
102867 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
102896 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
102925 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
102941 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:103427 original size:79 final size:79
Alignment explanation
Indices: 103249--103522 Score: 275
Period size: 79 Copynumber: 3.5 Consensus size: 79
103239 TTGAATGATG
** * * **
103249 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAG-GCA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCT-AGTGA-TATATCCGGGCTAA-CCCCGAAGAGCA
** * * *
103311 TTTGTGCGAGTTACTAAA
63 TTCATGCTAGTGA-TATA
* **
103329 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCGAAGAGCATTC
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATATCCGGGCTAACCCCGAAGAGCATTC
*
103394 ATGCTAGTGATGTA
66 ATGCTAGTGATATA
* * *
103408 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATCCGTGCTAACCCCGAAGAGCATTC
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATATCCGGGCTAACCCCGAAGAGCATTC
* * *
103473 GTGCTGGTGTTATA
66 ATGCTAGTGATATA
* * *
103487 TCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
103523 CGTGTATTCG
Statistics
Matches: 164, Mismatches: 27, Indels: 7
0.83 0.14 0.04
Matches are distributed among these distances:
79 109 0.66
80 42 0.26
81 7 0.04
82 6 0.04
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATATCCGGGCTAACCCCGAAGAGCATTC
ATGCTAGTGATATA
Found at i:103518 original size:40 final size:40
Alignment explanation
Indices: 103249--103522 Score: 281
Period size: 40 Copynumber: 6.9 Consensus size: 40
103239 TTGAATGATG
** *
103249 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCT-AGTGA-TATA
* ** * * *
103289 TCCGGACTAAGAT-CCGAAG-GCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGAGCATTCATGCTAGTGA-TATA
*
103329 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
*
103369 TCCGGGCTAAGT-CCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* *
103408 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* * * * *
103448 TCCGTGCTAA-CCCCGAAGAGCATTCGTGCTGGTGTTATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* * *
103487 TCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
103523 CGTGTATTCG
Statistics
Matches: 203, Mismatches: 25, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
39 73 0.36
40 110 0.54
41 20 0.10
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
Found at i:106976 original size:46 final size:47
Alignment explanation
Indices: 106916--107377 Score: 602
Period size: 46 Copynumber: 10.1 Consensus size: 47
106906 GAAATGATAG
106916 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA-GTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
106962 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATTTGT-A
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
107008 T-AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA--CG-
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
107051 T---G----ATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
107091 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
107138 -AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG---TATATATGTGA
107187 TAAGGCCTAATGGCCGATGTGATG-ATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
*
107235 TAGGGCCTAATGGCCGATGTGATG-ATGTG-AAGTGTATTATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA-TATATGTGA
*
107281 TAGGGCCTAATGG-CGATGTGATGAATGTGAAAGTGGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT-GTATATATGTGA
** * * * * * *
107328 -CGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
107374 TAAG
1 TAAG
107378 TCCCGAAGGG
Statistics
Matches: 378, Mismatches: 16, Indels: 43
0.86 0.04 0.10
Matches are distributed among these distances:
37 33 0.09
39 1 0.00
40 1 0.00
41 1 0.00
43 2 0.01
45 51 0.13
46 125 0.33
47 77 0.20
48 43 0.11
49 21 0.06
50 23 0.06
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:107372 original size:93 final size:94
Alignment explanation
Indices: 107053--107377 Score: 444
Period size: 93 Copynumber: 3.4 Consensus size: 94
107043 TATATACGTG
* *
107053 ATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAAT
1 ATGGCCGATGTGATGAATGTGAAAGTGTATAAATGTGATAAGGCCTAATGGCCGATGTGATGAAT
* *
107118 GTGAAAGT-GTATATACGTGAAAGGCCTA
66 GTGAAAGTGGTATATATGTGAAGGGCCTA
107146 ATGGCCGATGTGATGAATGTGAAAGTGTAATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 ATGGCCGATGTGATGAATGTGAAAGTGT-ATA-A-ATGTGATAAGGCCTAATGGCCGATGTGATG
*
107211 -ATGTGAAAGTGTATATATATGTGATAGGGCCTA
63 AATGTGAAAGTG-GTATATATGTGA-AGGGCCTA
* *
107244 ATGGCCGATGTGATG-ATGTG-AAGTGTATTATATGTGATAGGGCCTAATGG-CGATGTGATGAA
1 ATGGCCGATGTGATGAATGTGAAAGTGTA-TAAATGTGATAAGGCCTAATGGCCGATGTGATGAA
* *
107306 TGTGAAAGTGGTATATATGTGACGGGCCGA
65 TGTGAAAGTGGTATATATGTGAAGGGCCTA
* * * *
107336 GTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGGCCGATGTGATGAATGTGAAAGTGTATAAATGTGATAAG
107378 TCCCGAAGGG
Statistics
Matches: 207, Mismatches: 15, Indels: 20
0.86 0.06 0.08
Matches are distributed among these distances:
92 18 0.09
93 65 0.31
94 39 0.19
95 11 0.05
96 37 0.18
97 15 0.07
98 22 0.11
ACGTcount: A:0.31, C:0.09, G:0.32, T:0.29
Consensus pattern (94 bp):
ATGGCCGATGTGATGAATGTGAAAGTGTATAAATGTGATAAGGCCTAATGGCCGATGTGATGAAT
GTGAAAGTGGTATATATGTGAAGGGCCTA
Found at i:107568 original size:35 final size:37
Alignment explanation
Indices: 107495--107571 Score: 104
Period size: 36 Copynumber: 2.1 Consensus size: 37
107485 CCGAGCTCTA
* * *
107495 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
107532 AAGACCC-ATAACTTCGTGTGGAGATTATGT-CGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
107567 AAGAC
1 AAGAC
107572 TTCGTAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
35 10 0.28
36 19 0.53
37 7 0.19
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Done.