Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4256.1
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: 72081
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.29
Warning! 602 characters in sequence are not A, C, G, or T
Found at i:1840 original size:39 final size:40
Alignment explanation
Indices: 1689--1858 Score: 218
Period size: 40 Copynumber: 4.3 Consensus size: 40
1679 GGACTAAGAT
* *
1689 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACTAAA-TCCGGGTTAAGTC
*
1729 CCGAAGGCCTTCGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* * *
1769 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* * * * *
1809 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
1848 CCGAAGGCATT
1 CCGAAGGCATT
1859 TGAACGAGGA
Statistics
Matches: 118, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
39 35 0.30
40 80 0.68
41 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
Found at i:1878 original size:79 final size:80
Alignment explanation
Indices: 1716--1893 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
1706 AGATACAAAT
* * * *
1716 TCCGGGTTAAGCCCCGAAGGCCTTCGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
1781 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * * *
1796 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
1860 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
1875 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
1894 TACGTGATTT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
78 15 0.19
79 45 0.56
80 21 0.26
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:8476 original size:136 final size:136
Alignment explanation
Indices: 8310--8580 Score: 515
Period size: 136 Copynumber: 2.0 Consensus size: 136
8300 AAAAGCTCTC
*
8310 ATGTTGTTCTTGGCCGAATAGGAGAAAGAAAAAGAAGGAAGAAGAGCTTTGAGGAAATCGGCTAT
1 ATGTTGTTCTTGGCCGAATAGGAGAAAGAAAAAGAAGGAAAAAGAGCTTTGAGGAAATCGGCTAT
**
8375 GGTGGTTTGATAGACTAAGGTATGTTTGATTTTGTTCCATGAGATGCATGCATGTTTTAGTAGTT
66 GGTGGTTTGATAGACTAAGGTATGTTTGATGATGTTCCATGAGATGCATGCATGTTTTAGTAGTT
8440 AGCTTG
131 AGCTTG
8446 ATGTTGTTCTTGGCCGAATAGGAGAAAGAAAAAGAAGGAAAAAGAGCTTTGAGGAAATCGGCTAT
1 ATGTTGTTCTTGGCCGAATAGGAGAAAGAAAAAGAAGGAAAAAGAGCTTTGAGGAAATCGGCTAT
8511 GGTGGTTTGATAGACTAAGGTATGTTTGATGATGTTCCATGAGATGCATGCATGTTTTAGTAGTT
66 GGTGGTTTGATAGACTAAGGTATGTTTGATGATGTTCCATGAGATGCATGCATGTTTTAGTAGTT
8576 AGCTT
131 AGCTT
8581 CAGTTCTAAA
Statistics
Matches: 132, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
136 132 1.00
ACGTcount: A:0.30, C:0.09, G:0.29, T:0.32
Consensus pattern (136 bp):
ATGTTGTTCTTGGCCGAATAGGAGAAAGAAAAAGAAGGAAAAAGAGCTTTGAGGAAATCGGCTAT
GGTGGTTTGATAGACTAAGGTATGTTTGATGATGTTCCATGAGATGCATGCATGTTTTAGTAGTT
AGCTTG
Found at i:9876 original size:40 final size:40
Alignment explanation
Indices: 9817--10106 Score: 326
Period size: 40 Copynumber: 7.3 Consensus size: 40
9807 CATTTGAATG
* * *
9817 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATT
*
9857 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGATT
* *
9897 ATATCCGGGCT--GACCCGAAGGCATTTGTTCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGATT
* * *
9935 ATA-CACGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
1 ATATC-CGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATT
*
9975 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGATT
*
10015 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGATT
* * * ** *
10055 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATT
10095 ATATCC-GGCTAA
1 ATATCCGGGCTAA
10107 ATTCCGAAGA
Statistics
Matches: 216, Mismatches: 24, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
37 1 0.00
38 33 0.15
39 9 0.04
40 166 0.77
41 7 0.03
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATT
Found at i:13368 original size:39 final size:40
Alignment explanation
Indices: 13217--13386 Score: 218
Period size: 40 Copynumber: 4.3 Consensus size: 40
13207 GGACTAAGAT
* *
13217 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACTAAA-TCCGGGTTAAGTC
*
13257 CCGAAGGCCTTCGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* * *
13297 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* * * * *
13337 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
13376 CCGAAGGCATT
1 CCGAAGGCATT
13387 TGAACGAGGA
Statistics
Matches: 118, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
39 35 0.30
40 80 0.68
41 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
Found at i:13406 original size:79 final size:80
Alignment explanation
Indices: 13244--13421 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
13234 AGATACAAAT
* * * *
13244 TCCGGGTTAAGCCCCGAAGGCCTTCGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
13309 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * * *
13324 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
13388 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
13403 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
13422 TACGTGATTT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
78 15 0.19
79 45 0.56
80 21 0.26
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:19296 original size:150 final size:150
Alignment explanation
Indices: 19025--19324 Score: 582
Period size: 150 Copynumber: 2.0 Consensus size: 150
19015 CGAAATCTCC
*
19025 GAACGAGTTGGTCCAGTTGCGTATCGATTGATTTTGCCCCCTGAACTTGAAAAGATTCACGACGT
1 GAACGAGTTGGTCCAGTTGCGTATCGATTAATTTTGCCCCCTGAACTTGAAAAGATTCACGACGT
19090 CTTTCATGTTTCGATGCTTCGACGCTATAGATCTGATCCATCGCACATAATTAGCCCATCAGAGG
66 CTTTCATGTTTCGATGCTTCGACGCTATAGATCTGATCCATCGCACATAATTAGCCCATCAGAGG
19155 TTGAAATTCAAGCCGATATG
131 TTGAAATTCAAGCCGATATG
*
19175 GAACGGGTTGGTCCAGTTGCGTATCGATTAATTTTGCCCCCTGAACTTGAAAAGATTCACGACGT
1 GAACGAGTTGGTCCAGTTGCGTATCGATTAATTTTGCCCCCTGAACTTGAAAAGATTCACGACGT
19240 CTTTCATGTTTCGATGCTTCGACGCTATAGATCTGATCCATCGCACATAATTAGCCCATCAGAGG
66 CTTTCATGTTTCGATGCTTCGACGCTATAGATCTGATCCATCGCACATAATTAGCCCATCAGAGG
19305 TTGAAATTCAAGCCGATATG
131 TTGAAATTCAAGCCGATATG
19325 AGTTATGAAG
Statistics
Matches: 148, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
150 148 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (150 bp):
GAACGAGTTGGTCCAGTTGCGTATCGATTAATTTTGCCCCCTGAACTTGAAAAGATTCACGACGT
CTTTCATGTTTCGATGCTTCGACGCTATAGATCTGATCCATCGCACATAATTAGCCCATCAGAGG
TTGAAATTCAAGCCGATATG
Found at i:19643 original size:56 final size:56
Alignment explanation
Indices: 19557--19666 Score: 193
Period size: 56 Copynumber: 2.0 Consensus size: 56
19547 GACCCTAGTT
*
19557 GGAAAGCAGTTTCGGGACCGCTAAACCGAGTCACCAAATTATTTGAATGTGATATC
1 GGAAAGCAGTCTCGGGACCGCTAAACCGAGTCACCAAATTATTTGAATGTGATATC
* *
19613 GGAAAGCGGTCTCGGGACCGCTAGACCGAGTCACCAAATTATTTGAATGTGATA
1 GGAAAGCAGTCTCGGGACCGCTAAACCGAGTCACCAAATTATTTGAATGTGATA
19667 ATTATTGCCT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (56 bp):
GGAAAGCAGTCTCGGGACCGCTAAACCGAGTCACCAAATTATTTGAATGTGATATC
Found at i:19968 original size:56 final size:56
Alignment explanation
Indices: 19882--20001 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
19872 ACAGGGGATG
*
19882 ATGGGCAGAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
19938 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
19994 ATGGGCAA
1 ATGGGCAA
20002 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.43, C:0.09, G:0.25, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
Found at i:21212 original size:40 final size:39
Alignment explanation
Indices: 21168--21245 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
21158 AGTGACCATA
* *
21168 TCCGGACTAAGATCCGAAGGCATTTGTCCGAGTTACTAAT
1 TCCGGACTAAG-CCCGAAGGCATTGGTCCGAGTTACTAAT
* *
21208 TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 TCCGGACTAAGCCCGAAGGCATTGGTCCGAGTTACTAA
21246 ATCCTGAGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 24 0.71
40 10 0.29
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (39 bp):
TCCGGACTAAGCCCGAAGGCATTGGTCCGAGTTACTAAT
Found at i:21229 original size:39 final size:41
Alignment explanation
Indices: 21128--21249 Score: 119
Period size: 40 Copynumber: 3.1 Consensus size: 41
21118 TCGAATGATG
* ** * *
21128 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CATA
1 TCCGGGCTAAGACCCGAAGGCATTTGT-CCGAGTTACTAATA
* *
21168 TCCGGACTAAGATCCGAAGGCATTTGTCCGAGTTACTAAT-
1 TCCGGGCTAAGACCCGAAGGCATTTGTCCGAGTTACTAATA
* *
21208 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAA-A
1 TCCGGGCTAAGACCCGAAGGCATTTGTCCGAGTTACTAATA
21247 TCC
1 TCC
21250 TGAGTTACTA
Statistics
Matches: 68, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
39 27 0.40
40 34 0.50
41 7 0.10
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGACCCGAAGGCATTTGTCCGAGTTACTAATA
Found at i:31723 original size:22 final size:22
Alignment explanation
Indices: 31698--31739 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
31688 CAGAAGAAGG
* *
31698 AAAGAATAACAAATGGAGAGAA
1 AAAGAAAAACAAAAGGAGAGAA
*
31720 AAAGAAAAATAAAAGGAGAG
1 AAAGAAAAACAAAAGGAGAG
31740 GAAGAGTGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.67, C:0.02, G:0.24, T:0.07
Consensus pattern (22 bp):
AAAGAAAAACAAAAGGAGAGAA
Found at i:38310 original size:39 final size:39
Alignment explanation
Indices: 38256--38335 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
38246 TAGCTCGTTT
38256 ATCCACTGAGCGAATACTTATTTGTAAGGGCTCAACTAA
1 ATCCACTGAGCGAATACTTATTTGTAAGGGCTCAACTAA
38295 ATCCACTGAGCGAATACTTATTTGTAAGGGCTCAACTAA
1 ATCCACTGAGCGAATACTTATTTGTAAGGGCTCAACTAA
38334 AT
1 AT
38336 TCGACCACAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (39 bp):
ATCCACTGAGCGAATACTTATTTGTAAGGGCTCAACTAA
Found at i:38505 original size:40 final size:40
Alignment explanation
Indices: 38461--39392 Score: 1616
Period size: 40 Copynumber: 23.3 Consensus size: 40
38451 GCTCCTCGTT
* * *
38461 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
38501 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
38541 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAAATCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
38581 CAAATGCCTTCCGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
38621 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAAATCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
38661 CAAATGCCTTCCGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
38701 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAAATCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
38741 CAAATGCCTTCCGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
38781 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAAATCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
38821 CAAATGCCTTCCGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
38861 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAAATCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
38901 CAAATGCCTTCCGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
38941 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAAATCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
38981 CAAATGCCTTCCGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
39021 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAAATCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
39061 CAAATGCCTTCCGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
39101 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAAATCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
39141 CAAATGCCTTCCGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
39181 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAAATCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
39221 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
39261 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAAATCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
39301 CAAATGCCTTCCGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
39341 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
39380 CAAATGCCTTCGG
1 CAAATGCCTTCGG
39393 ATCTTAGTCC
Statistics
Matches: 847, Mismatches: 44, Indels: 3
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 0.04
40 810 0.96
41 2 0.00
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:42304 original size:28 final size:27
Alignment explanation
Indices: 42249--42360 Score: 122
Period size: 27 Copynumber: 4.1 Consensus size: 27
42239 AGCATGGCTG
* * *
42249 CCAGAACAGATAA-AGTGACAGAGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
*
42275 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAATTGTGGCAGAGCCA
42303 CCAGAACAGA-AATATGTGGCAGAGCCA
1 CCAGAACAGATAAT-TGTGGCAGAGCCA
* *
42330 CCA-AATTAGATAATTGTGGCATAGCCA
1 CCAGAA-CAGATAATTGTGGCAGAGCCA
42357 CCAG
1 CCAG
42361 GACGCTTCGT
Statistics
Matches: 74, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
26 10 0.14
27 46 0.62
28 18 0.24
ACGTcount: A:0.39, C:0.22, G:0.23, T:0.15
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:42341 original size:54 final size:54
Alignment explanation
Indices: 42249--42360 Score: 138
Period size: 54 Copynumber: 2.1 Consensus size: 54
42239 AGCATGGCTG
* *
42249 CCAGAACAGATAAAGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATAAAGTGACAGAGCCACCAAATACAGATAATCGTGGCAGAGCCA
* * * *
42303 CCAGAACAGA-AATATGTGGCAGAGCCACCAAAT-TAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-A-GTGACAGAGCCACCAAATACAGATAATCGTGGCAGAGCCA
42357 CCAG
1 CCAG
42361 GACGCTTCGT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
53 2 0.04
54 33 0.66
55 15 0.30
ACGTcount: A:0.39, C:0.22, G:0.23, T:0.15
Consensus pattern (54 bp):
CCAGAACAGATAAAGTGACAGAGCCACCAAATACAGATAATCGTGGCAGAGCCA
Found at i:43625 original size:22 final size:22
Alignment explanation
Indices: 43580--43626 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
43570 GGGGAACAGA
* * *
43580 AGAAGAAAAGAAGAACAAATGG
1 AGAAAAAAAGAAAAACAAAAGG
*
43602 AGAAAAAAAGAAAAATAAAAGG
1 AGAAAAAAAGAAAAACAAAAGG
43624 AGA
1 AGA
43627 GGAAGAGTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.70, C:0.02, G:0.23, T:0.04
Consensus pattern (22 bp):
AGAAAAAAAGAAAAACAAAAGG
Found at i:50747 original size:46 final size:46
Alignment explanation
Indices: 50675--50762 Score: 149
Period size: 46 Copynumber: 1.9 Consensus size: 46
50665 GGAAAGAGCC
* *
50675 AATCTCCCTTACAGTTGTGGGGTATGGCAGCGAGTTAATGATAGTG
1 AATCACCCTTACAGTTGTGGGGTATGGCAGCAAGTTAATGATAGTG
*
50721 AATCACCCTTATAGTTGTGGGGTATGGCAGCAAGTTAATGAT
1 AATCACCCTTACAGTTGTGGGGTATGGCAGCAAGTTAATGAT
50763 GTCAATCTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (46 bp):
AATCACCCTTACAGTTGTGGGGTATGGCAGCAAGTTAATGATAGTG
Found at i:52358 original size:23 final size:23
Alignment explanation
Indices: 52332--52379 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
52322 TGACACTACC
52332 TATTTTACAAGATATGAAAAACA
1 TATTTTACAAGATATGAAAAACA
52355 TATTTTACAAGATATGAAAAACA
1 TATTTTACAAGATATGAAAAACA
52378 TA
1 TA
52380 CATTGGTCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.31
Consensus pattern (23 bp):
TATTTTACAAGATATGAAAAACA
Found at i:55969 original size:40 final size:40
Alignment explanation
Indices: 54997--55962 Score: 1828
Period size: 40 Copynumber: 24.2 Consensus size: 40
54987 AACCGAAGTA
* * *
54997 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATA
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* *
55036 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAGATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* *
55076 CCTTCGGGACATAGCCTGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
55116 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
55156 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
55196 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
55236 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
55276 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
55316 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
55356 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
55396 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
55436 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
55476 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
55516 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
55556 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
55596 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
55636 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
55676 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
55716 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
55756 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
55796 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* *
55836 CCTTCGGGACTTAGCCCGGATATAGTAACTAGAACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
55876 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
55916 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
55956 CCTTCGG
1 CCTTCGG
55963 ATCTTAGTCC
Statistics
Matches: 910, Mismatches: 15, Indels: 3
0.98 0.02 0.00
Matches are distributed among these distances:
39 13 0.01
40 897 0.99
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:57357 original size:13 final size:13
Alignment explanation
Indices: 57339--57364 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
57329 ATTTTTATTT
57339 TTAACATAAAATA
1 TTAACATAAAATA
57352 TTAACATAAAATA
1 TTAACATAAAATA
57365 ATTAGAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAACATAAAATA
Found at i:63272 original size:40 final size:40
Alignment explanation
Indices: 63198--63402 Score: 308
Period size: 40 Copynumber: 5.2 Consensus size: 40
63188 AACCGAAGTA
* * *
63198 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATA
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
63237 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
63277 CCTTCGAGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* * *
63317 CCTTCGAGACTTATCCCGGA-ATAGTAACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
63356 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
63396 CTTTCGG
1 CCTTCGG
63403 ATCTTAGTCC
Statistics
Matches: 153, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
39 49 0.32
40 103 0.67
41 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:63353 original size:79 final size:80
Alignment explanation
Indices: 63198--63414 Score: 307
Period size: 79 Copynumber: 2.7 Consensus size: 80
63188 AACCGAAGTA
* * * *
63198 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATACCTTCGGGACTTAGCCCGGATATA
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGCCTTCGAGACTTAGCCCGGATATA
*
63261 GTCACTAGCACAAATG
65 GTAACTAGCACAAATG
* *
63277 CCTTCGAGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGAGACTTATCCCGGA-ATAG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGAGACTTAGCCCGGATATAG
63341 TAACTAGCACAAATG
66 TAACTAGCACAAATG
* *
63356 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCTTTCG-GATCTTAGTCCGG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGAGA-CTTAGCCCGG
63415 TTATCATCCG
Statistics
Matches: 124, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
78 2 0.02
79 82 0.66
80 39 0.31
81 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGAGACTTAGCCCGGATATAG
TAACTAGCACAAATG
Found at i:64371 original size:74 final size:74
Alignment explanation
Indices: 64250--64396 Score: 240
Period size: 74 Copynumber: 2.0 Consensus size: 74
64240 ATATCTCCCT
* *
64250 GTACAGGGCTTCATTACTGATGTCGTTTGTTTCGATAGAAACTAGACTAAAAAAGGAATCTATTC
1 GTACAGGGCTTCAATACTGATGTCGTTTGTTTCGATAGAAACTAGACTAAAAAAGGAATCTATGC
64315 ATATATGGC
66 ATATATGGC
* * * *
64324 GTACAGGGCTTCAATACTGATGTGGTTTGTTTCTATAGAAACTAGACTCAAAAGGGAATCTATGC
1 GTACAGGGCTTCAATACTGATGTCGTTTGTTTCGATAGAAACTAGACTAAAAAAGGAATCTATGC
64389 ATATATGG
66 ATATATGG
64397 AATGACTTCT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 67 1.00
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (74 bp):
GTACAGGGCTTCAATACTGATGTCGTTTGTTTCGATAGAAACTAGACTAAAAAAGGAATCTATGC
ATATATGGC
Found at i:64796 original size:41 final size:40
Alignment explanation
Indices: 64669--64813 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
64659 CTCGCACAAG
* * * * *
64669 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
64709 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
64749 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
64790 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
64814 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.64
41 27 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Done.