Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold376
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: 900718
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 6 of 6
Found at i:864317 original size:19 final size:20
Alignment explanation
Indices: 864293--864344 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
864283 CTTAACTGTT
864293 TGTATCGATACAT-A-CAAGA
1 TGTATCGATACATGACCAA-A
*
864312 TGTATCGATACGTGACCAAA
1 TGTATCGATACATGACCAAA
864332 TGTATCGATACAT
1 TGTATCGATACAT
864345 TGGCTTGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 12 0.41
20 14 0.48
21 3 0.10
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (20 bp):
TGTATCGATACATGACCAAA
Found at i:872858 original size:13 final size:13
Alignment explanation
Indices: 872840--872864 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
872830 ATAATGCACA
872840 GTATCGATACATT
1 GTATCGATACATT
872853 GTATCGATACAT
1 GTATCGATACAT
872865 GACCACTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:872861 original size:33 final size:32
Alignment explanation
Indices: 872819--872881 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
872809 CACCTTCAGA
*
872819 TGTATCGATACATAATGCACAGTATCGATACAT
1 TGTATCGATACATAA-CCACAGTATCGATACAT
* *
872852 TGTATCGATACATGACCACTGTATCGATAC
1 TGTATCGATACATAACCACAGTATCGATAC
872882 TTGCAAAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (32 bp):
TGTATCGATACATAACCACAGTATCGATACAT
Found at i:872977 original size:20 final size:19
Alignment explanation
Indices: 872934--872985 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
872924 CTTAACTATT
*
872934 TGTATTGATACATACAAGA
1 TGTATCGATACATACAAGA
872953 TGTATCGATACATGACCAA-A
1 TGTATCGATACAT-A-CAAGA
*
872973 TGTATCTATACAT
1 TGTATCGATACAT
872986 TGGCTTGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 12 0.41
20 14 0.48
21 3 0.10
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (19 bp):
TGTATCGATACATACAAGA
Found at i:874280 original size:12 final size:10
Alignment explanation
Indices: 874248--874292 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
874238 TAAATTTCTT
*
874248 ATTTTTTAGA
1 ATTTTTTAAA
874258 ATTTTTTAAA
1 ATTTTTTAAA
874268 ATTTTTCTGAAA
1 ATTTTT-T-AAA
*
874280 ATTTTTGAAA
1 ATTTTTTAAA
874290 ATT
1 ATT
874293 AATCGTCATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 21 0.68
11 1 0.03
12 9 0.29
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.56
Consensus pattern (10 bp):
ATTTTTTAAA
Found at i:874339 original size:43 final size:43
Alignment explanation
Indices: 874281--874373 Score: 177
Period size: 43 Copynumber: 2.1 Consensus size: 43
874271 TTTCTGAAAA
874281 TTTTTGAAAATTAATCGTCATATATTTTACCAATACCTATATAG
1 TTTTT-AAAATTAATCGTCATATATTTTACCAATACCTATATAG
874325 TTTTTAAAATTAATCGTCATATATTTTACCAATACCTATATAG
1 TTTTTAAAATTAATCGTCATATATTTTACCAATACCTATATAG
874368 TTTTTA
1 TTTTTA
874374 TGCCAATACG
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 44 0.90
44 5 0.10
ACGTcount: A:0.35, C:0.13, G:0.05, T:0.46
Consensus pattern (43 bp):
TTTTTAAAATTAATCGTCATATATTTTACCAATACCTATATAG
Found at i:875011 original size:165 final size:167
Alignment explanation
Indices: 874709--875052 Score: 407
Period size: 166 Copynumber: 2.1 Consensus size: 167
874699 ATTTCAAACA
* *
874709 TTAAAATTCTTTAAATATTATCATTTAATAACCATTAAATCAGTTTTGAAAAATTCTTTTTATTT
1 TTAAAATTCATCAAATATTATCATTTAATAACCATTAAATCAGTTTTGAAAAATTCTTTTTATTT
* * * * *
874774 TATGAGTTATTGATTTTCTTTTAGAATTTCTTCTTATTTTCGAAATACGGAGTTTTCTTCTCCAT
66 TATAAGTTATTGATTTTCTTTTAGAATATCTTCCTATTTTCGAAAAACGGAGTTTTCTACTCCAT
* *
874839 AAATA-TTTTGAGAGGATTCTGATCGATTTTAAATTT
131 AAATATTTTTGAGAGGATTCTCATCGATTTAAAATTT
* *
874875 TTAAAATTCATCAAATATTATCATTTGAT-TCACATTAAATCAGTTTT-AAAAATT-TTATTTAT
1 TTAAAATTCATCAAATATTATCATTTAATAAC-CATTAAATCAGTTTTGAAAAATTCTT-TTTAT
* *
874937 TTTCATAAGTT-TTGAATTTTTTTCTTTA-AA-ATC-TCCTATTTTTGAAAAACGGAGTTTTCTA
64 TTT-ATAAGTTATTG-A-TTTTCT-TTTAGAATATCTTCCTATTTTCGAAAAACGGAGTTTTCTA
* * * * *
874998 CTTCATAAATATTTTTGGGAGGATTTTCTTCGGTTTAAAATTT
125 CTCCATAAATATTTTTGAGAGGATTCTCATCGATTTAAAATTT
*
875041 TTAAAACTCATC
1 TTAAAATTCATC
875053 TAATTATTGT
Statistics
Matches: 152, Mismatches: 19, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
164 2 0.01
165 53 0.35
166 86 0.57
167 7 0.05
168 4 0.03
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.49
Consensus pattern (167 bp):
TTAAAATTCATCAAATATTATCATTTAATAACCATTAAATCAGTTTTGAAAAATTCTTTTTATTT
TATAAGTTATTGATTTTCTTTTAGAATATCTTCCTATTTTCGAAAAACGGAGTTTTCTACTCCAT
AAATATTTTTGAGAGGATTCTCATCGATTTAAAATTT
Found at i:877254 original size:310 final size:310
Alignment explanation
Indices: 876677--877280 Score: 735
Period size: 310 Copynumber: 1.9 Consensus size: 310
876667 GGGTTACCGG
* * * *
876677 GATACTTTTATGTCGAAGGTATACCCCTATGGGCATTTTCATAATTTTTCAGAATCGAGTCCTAG
1 GATACTTCTAAGTCGAAGGTATACCCCTATGGGCATTTTCATAATTTTTCAAAATCAAGTCCTAG
* * ** *
876742 TTGTCACTGGTTTGCTTTTATGTTGAAAGTAGGTATTTAGGATAGGTTCATCCCATTTATAATCC
66 TTGTCACGGGTTCGCTTTTATGTCCAAAGTAGGTATTTAGGATAAGTTCATCCCATTTATAATCC
* * * *
876807 TTTTTAAGTCTTTTAGGGGTATTAGGCACTTCTACATCGAAAATATCACCTAGGGATATTTTTTG
131 TTTTTAAGTCCTTTAGGGGTATCAGGCACTTCTACATCGAAAATATCACCTAGGGACATTTTTCG
* * * *
876872 TAATTTTCTAGAGTTGAGTCTTAGGTTGTCACCAGGTTTGCATTTATGCCGAAGGTGGGGATTTT
196 TAATTTTCTAGAATCGAGTCTTAGGTTGTCACCAGGTTAGCATTTATGCCGAAAGTGGGGATTTT
876937 AGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCCTCTAAGGGTATCA
261 AGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCCTCTAAGGGTATCA
* *
876987 GATACTTCTAAGTCGAAGGTAT-CTCCTATGGGTATTTTCATAA-TTTTCTAAAA-CTAAGTCCT
1 GATACTTCTAAGTCGAAGGTATACCCCTATGGGCATTTTCATAATTTTTC-AAAATC-AAGTCCT
* *
877049 AGGTTGTCACCGGGTTCGCTTTTATG-CCAAATGTGGGTATTTAGGATAAGTTCATTCCATCCTT
64 A-GTTGTCA-CGGGTTCGCTTTTATGTCCAAA-GTAGGTATTTAGGATAAGTTCATCCCAT--TT
* * * ** *
877113 -TTA-CCTTTTTAAGTCCTTTA-GGGTGTCGGGCACTTCTACATCGAAGGTATCCCCTATGGG-C
124 ATAATCCTTTTTAAGTCCTTTAGGGGTATCAGGCACTTCTACATCGAAAATATCACCTA-GGGAC
* * ** *
877174 A-TTTTCGTAATTTTTTTATAATCGAGTCTTAGGTTGTCA-TTGAGTTAGCTTTTATGCCGAAAG
188 ATTTTTCGTAA-TTTTCTAGAATCGAGTCTTAGGTTGTCACCAG-GTTAGCATTTATGCCGAAAG
*
877237 TGGGTA-TTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAG
251 TGGGGATTTTA-GATAGGTTCATCCCATCTATAATCCTTTTTAAG
877281 CCTTTTAGGA
Statistics
Matches: 250, Mismatches: 33, Indels: 22
0.82 0.11 0.07
Matches are distributed among these distances:
308 6 0.02
309 42 0.17
310 140 0.56
311 58 0.23
312 2 0.01
313 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.40
Consensus pattern (310 bp):
GATACTTCTAAGTCGAAGGTATACCCCTATGGGCATTTTCATAATTTTTCAAAATCAAGTCCTAG
TTGTCACGGGTTCGCTTTTATGTCCAAAGTAGGTATTTAGGATAAGTTCATCCCATTTATAATCC
TTTTTAAGTCCTTTAGGGGTATCAGGCACTTCTACATCGAAAATATCACCTAGGGACATTTTTCG
TAATTTTCTAGAATCGAGTCTTAGGTTGTCACCAGGTTAGCATTTATGCCGAAAGTGGGGATTTT
AGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCCTCTAAGGGTATCA
Found at i:877288 original size:155 final size:155
Alignment explanation
Indices: 876689--877289 Score: 634
Period size: 155 Copynumber: 3.9 Consensus size: 155
876679 TACTTTTATG
*
876689 TCGAAGGTATACCCCTATGGGCATTTTCATAATTTT-TCAGAATCGAGTCCTA-GTTGTCACTG-
1 TCGAAGGTAT-CCCCTATGGGCATTTTCATAATTTTCT-AGAATCGAGTCCTAGGTTGTCACCGA
** * *
876751 GTTTGCTTTTATGTTGAAAGTAGGTATTTAGGATAGGTTCATCCCATTTATAATCCTTTTTAAGT
64 GTTTGCTTTTATGCCGAAAGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGT
*
876816 -CTTTTAGGGGTATTAGGCACTTCTACA
129 CCTTTTA-GGGTATCAGGCACTTCTACA
** * * ** * * *
876843 TCGAAAATATCACCTA-GGGATATTTTTTGTAATTTTCTAGAGTTGAGTCTTAGGTTGTCACC-A
1 TCGAAGGTATCCCCTATGGG-CA-TTTTCATAATTTTCTAGAATCGAGTCCTAGGTTGTCACCGA
* * *
876906 GGTTTGCATTTATGCCGAAGGTGGGGATTTTA-GATAGGTTCATCCCATCTATAATCCTTTTTAA
64 -GTTTGCTTTTATGCCGAAAGTGGGTA-TTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAA
* * **
876970 GTCCTCTAAGGGTATCAGATACTTCTA-A
127 GTCCTTTTAGGGTATCAGGCACTTCTACA
* * * * *
876998 GTCGAAGGTATCTCCTATGGGTATTTTCATAATTTTCTA-AAACTAAGTCCTAGGTTGTCACCGG
1 -TCGAAGGTATCCCCTATGGGCATTTTCATAATTTTCTAGAATC-GAGTCCTAGGTTGTCACCGA
* * * * *
877062 GTTCGCTTTTATGCC-AAATGTGGGTATTTAGGATAAGTTCATTCCATCCTTTTA-CCTTTTTAA
64 GTTTGCTTTTATGCCGAAA-GTGGGTATTTAGGATAGGTTCATCCCAT-CTATAATCCTTTTTAA
* *
877125 GTCC-TTTAGGGTGTCGGGCACTTCTACA
127 GTCCTTTTAGGGTATCAGGCACTTCTACA
* * * * **
877153 TCGAAGGTATCCCCTATGGGCATTTTCGTAATTTTTTTATAATCGAGTCTTAGGTTGTCATTGAG
1 TCGAAGGTATCCCCTATGGGCATTTTCATAA-TTTTCTAGAATCGAGTCCTAGGTTGTCACCGAG
*
877218 TTAGCTTTTATGCCGAAAGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAG-C
65 TTTGCTTTTATGCCGAAAGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTC
877282 CTTTTAGG
130 CTTTTAGG
877290 ATCAACGGGC
Statistics
Matches: 364, Mismatches: 62, Indels: 41
0.78 0.13 0.09
Matches are distributed among these distances:
152 3 0.01
153 6 0.02
154 87 0.24
155 164 0.45
156 93 0.26
157 11 0.03
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (155 bp):
TCGAAGGTATCCCCTATGGGCATTTTCATAATTTTCTAGAATCGAGTCCTAGGTTGTCACCGAGT
TTGCTTTTATGCCGAAAGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCC
TTTTAGGGTATCAGGCACTTCTACA
Found at i:880447 original size:20 final size:20
Alignment explanation
Indices: 880422--880476 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
880412 AATTGCCTAC
*
880422 ATGTATCGATACATTGAAGA
1 ATGTATCGATACATTGAAAA
* * *
880442 ATGTATCAATAAAATGAAAA
1 ATGTATCGATACATTGAAAA
880462 ATGTATCGATACATT
1 ATGTATCGATACATT
880477 TAGGTCAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:880633 original size:21 final size:20
Alignment explanation
Indices: 880583--880636 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
880573 CATTTCAGAC
*
880583 ATGTATCAATACATTCACTT
1 ATGTATCGATACATTCACTT
*
880603 ATGAATCGATACATTCACTT
1 ATGTATCGATACATTCACTT
880623 ATTGTATCGATACA
1 A-TGTATCGATACA
880637 AATTGTAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTCACTT
Found at i:885430 original size:28 final size:28
Alignment explanation
Indices: 885390--885461 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
885380 GGAATAAAGC
** *
885390 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
885418 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
885446 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
885462 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:885519 original size:52 final size:52
Alignment explanation
Indices: 885450--885831 Score: 250
Period size: 52 Copynumber: 7.3 Consensus size: 52
885440 AAATAACGAG
* * *
885450 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTAGTTTTGGAAATAAAACCGGA
** * * *
885502 GTTGGAGTATCCCCGATTAAAGGAAAATTGG-CGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTAGTTTTGGAAATAAAACC-GGA
*
885555 -TTGGAGTATCCCCGATTGTGGAAAAATTAGT-GTTTT--AACGATAAAACCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTAGTTTTGGAA--ATAAAACCGGA
** *** * ***** *
885606 GTTGGAGTATCCCCTCGAAAGT-AACGGGGTTGG-AGTATCCCCGATGAAATAAC-GA
1 GTTGGAGTAT-CCC-CGATTGTGAA--AAATTGGTAGTTTTGGAAAT-AAA-ACCGGA
* * *
885661 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 -GTTGGAGTATCCCCGATTGTGAAAAATTGGTAGTTTTGGAAATAAAACCGGA
** * * *
885714 GTTGGAGTATCCCCGATTAAAGGAAAATTGG-CGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTAGTTTTGGAAATAAAACC-GGA
*
885767 -TTGGAGTATCCCCGATTGTGGAAAAATTAGT-GTTTT--AACGATAAAACCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTAGTTTTGGAA--ATAAAACCGGA
885818 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
885832 TCGAAAATAA
Statistics
Matches: 254, Mismatches: 49, Indels: 54
0.71 0.14 0.15
Matches are distributed among these distances:
50 4 0.02
51 6 0.02
52 164 0.65
53 36 0.14
54 23 0.09
55 9 0.04
56 12 0.05
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.28
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTAGTTTTGGAAATAAAACCGGA
Found at i:885599 original size:104 final size:103
Alignment explanation
Indices: 885451--885831 Score: 402
Period size: 104 Copynumber: 3.6 Consensus size: 103
885441 AATAACGAGG
* * * *
885451 TTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
1 TTGGAGTATCCCCGATTGTGAAAAATTAGTAGTTTT-GAAATAAAACCGGAGTTGGAGTATCCCC
885516 GATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA
65 GATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA
885555 TTGGAGTATCCCCGATTGTGGAAAAATTAGT-GTTTT-AACGATAAAACCGGAGTTGGAGTATCC
1 TTGGAGTATCCCCGATTGT-GAAAAATTAGTAGTTTTGAA--ATAAAACCGGAGTTGGAGTATCC
* * ** * ** *
885618 CC--TCGAAAGTAACGGGGTTGGAGTATCCCCGATGAAAT--AACGAGG-
63 CCGAT-TAAAGGAA---AATTGGCGT-T--TTGA--AAATAAAACCAGGA
* * * *
885663 TTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
1 TTGGAGTATCCCCGATTGTGAAAAATTAGTAGTTTT-GAAATAAAACCGGAGTTGGAGTATCCCC
885728 GATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA
65 GATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA
885767 TTGGAGTATCCCCGATTGTGGAAAAATTAGT-GTTTT-AACGATAAAACCGGAGTTGGAGTATCC
1 TTGGAGTATCCCCGATTGT-GAAAAATTAGTAGTTTTGAA--ATAAAACCGGAGTTGGAGTATCC
885830 CC
63 CC
885832 TCGAAAATAA
Statistics
Matches: 226, Mismatches: 28, Indels: 46
0.75 0.09 0.15
Matches are distributed among these distances:
101 4 0.02
102 5 0.02
103 14 0.06
104 92 0.41
105 21 0.09
106 12 0.05
107 11 0.05
108 46 0.20
109 14 0.06
110 3 0.01
111 4 0.02
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.28
Consensus pattern (103 bp):
TTGGAGTATCCCCGATTGTGAAAAATTAGTAGTTTTGAAATAAAACCGGAGTTGGAGTATCCCCG
ATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA
Found at i:885630 original size:212 final size:212
Alignment explanation
Indices: 885383--885945 Score: 1011
Period size: 212 Copynumber: 2.6 Consensus size: 212
885373 TATTTTGGGA
* * *
885383 ATAAAGCCGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACG
1 ATAAAACCGGAGTTGGAGTATCCCCTCGAAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACG
885448 AGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATC
66 AGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATC
885513 CCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGATTGGAGTATCCCCGATTGTGGAA
131 CCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGATTGGAGTATCCCCGATTGTGGAA
885578 AAATTAGTGTTTTAACG
196 AAATTAGTGTTTTAACG
885595 ATAAAACCGGAGTTGGAGTATCCCCTCGAAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACG
1 ATAAAACCGGAGTTGGAGTATCCCCTCGAAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACG
885660 AGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATC
66 AGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATC
885725 CCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGATTGGAGTATCCCCGATTGTGGAA
131 CCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGATTGGAGTATCCCCGATTGTGGAA
885790 AAATTAGTGTTTTAACG
196 AAATTAGTGTTTTAACG
* *
885807 ATAAAACCGGAGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACG
1 ATAAAACCGGAGTTGGAGTATCCCCTCGAAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACG
* * *
885871 GGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTATTTTTTTGGAAATAAAATCGGAGTTGGAAT
66 AGGTTGGAGTATCCTCGATTGTGAA-AAATTGGTA--TTTTTGGAAATAAAATCGGAGTTGGAGT
*
885936 ATCCTCGATT
128 ATCCCCGATT
885946 GTGGAGAATT
Statistics
Matches: 339, Mismatches: 9, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
211 29 0.09
212 274 0.81
214 36 0.11
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.28
Consensus pattern (212 bp):
ATAAAACCGGAGTTGGAGTATCCCCTCGAAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACG
AGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATC
CCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGATTGGAGTATCCCCGATTGTGGAA
AAATTAGTGTTTTAACG
Found at i:885646 original size:28 final size:27
Alignment explanation
Indices: 885606--885673 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 27
885596 TAAAACCGGA
*
885606 GTTGGAGTATCCCC-TCGAAAGTAACGGG
1 GTTGGAGTATCCCCAT-GAAA-TAACGAG
885634 GTTGGAGTATCCCCGATGAAATAACGAG
1 GTTGGAGTATCCCC-ATGAAATAACGAG
885662 GTTGGAGTATCC
1 GTTGGAGTATCC
885674 TCGATTGTGA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
28 32 0.86
29 4 0.11
30 1 0.03
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (27 bp):
GTTGGAGTATCCCCATGAAATAACGAG
Found at i:885850 original size:28 final size:28
Alignment explanation
Indices: 885805--885886 Score: 98
Period size: 27 Copynumber: 3.0 Consensus size: 28
885795 AGTGTTTTAA
* *
885805 CGATAAA-ACCGGAGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
885832 TCGA-AAATAACGGGGTTGGAGTAT-CCC
1 -CGATAAATAACGGGGTTGGAGTATCCCC
* *
885859 CGATGATTAACGGGGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
885887 GATTGTGAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 3 0.06
27 24 0.51
28 20 0.43
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (28 bp):
CGATAAATAACGGGGTTGGAGTATCCCC
Found at i:888318 original size:13 final size:13
Alignment explanation
Indices: 888300--888325 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
888290 ACAAAGATCC
888300 ATGTATCGATACA
1 ATGTATCGATACA
888313 ATGTATCGATACA
1 ATGTATCGATACA
888326 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:888321 original size:33 final size:33
Alignment explanation
Indices: 888279--888345 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
888269 AAAATTTCCA
***
888279 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
888312 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
888345 A
1 A
888346 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:888389 original size:19 final size:18
Alignment explanation
Indices: 888365--888432 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
888355 CAGTAGCTAA
888365 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
888384 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
888399 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
888416 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
888433 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:888405 original size:13 final size:13
Alignment explanation
Indices: 888387--888411 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
888377 ACAATACTTA
888387 TGTATCGATACAT
1 TGTATCGATACAT
888400 TGTATCGATACA
1 TGTATCGATACA
888412 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:888409 original size:32 final size:32
Alignment explanation
Indices: 888368--888430 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
888358 TAGCTAATTA
*
888368 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
888400 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
888431 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:888512 original size:21 final size:21
Alignment explanation
Indices: 888488--888544 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
888478 CATTTGTAGG
888488 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
888509 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
888530 ATGTATCGATACATT
1 ATGTATCGATACATT
888545 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:888555 original size:1 final size:1
Alignment explanation
Indices: 888549--888596 Score: 69
Period size: 1 Copynumber: 48.0 Consensus size: 1
888539 TACATTTAAA
***
888549 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTCAATTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
888597 CAAACACTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.04, C:0.02, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:888597 original size:19 final size:19
Alignment explanation
Indices: 888549--888599 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
888539 TACATTTAAA
888549 TTTTTTTTTTTTT---TTT
1 TTTTTTTTTTTTTCAATTT
888565 TTTTTTTTTTTTTCAATTT
1 TTTTTTTTTTTTTCAATTT
888584 TTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTCAA
888600 ACACTTTATC
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
16 13 0.41
19 19 0.59
ACGTcount: A:0.08, C:0.04, G:0.00, T:0.88
Consensus pattern (19 bp):
TTTTTTTTTTTTTCAATTT
Found at i:889277 original size:55 final size:55
Alignment explanation
Indices: 889193--889927 Score: 1074
Period size: 55 Copynumber: 13.3 Consensus size: 55
889183 ATAAATTGTA
* * * * * *
889193 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
889248 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCCACTTGTGTGGGCTTTGAAAAGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
889303 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
889358 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
889413 TCCTGTTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
** *
889468 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
889523 TCCTGCTCTTTGAGGATTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
889578 TCCTGCTCTTTGAGGACT-AGAAGGCGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
889633 TCCTGCTCTTTGAGGACTGGAAAGGTGCCACCAACTTGTGTGGGCTTTGAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
889689 TCCTGCTCTTTGGGGACTGAAAAGGTGCCACCAACTTGTGTGGGCTTTGAGAGGTG
1 TCCTGCTCTTTGAGGACTG-AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
889745 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
889800 TCCTGCTCGTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
889855 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
889910 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
889928 AAAAAGCGGA
Statistics
Matches: 634, Mismatches: 32, Indels: 28
0.91 0.05 0.04
Matches are distributed among these distances:
54 11 0.02
55 506 0.80
56 115 0.18
57 2 0.00
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:889769 original size:26 final size:26
Alignment explanation
Indices: 889684--889770 Score: 70
Period size: 29 Copynumber: 3.2 Consensus size: 26
889674 GGGCTTTGAG
889684 AGGTGTCCTGCTCTTTGGGGACTGAAA
1 AGGTGTCCTGCTCTTTGGGGACTG-AA
** * *
889711 AGGTG-CCACCAACTTGTGTGGG-CTTTGAG
1 AGGTGTCCTGC-TCTT-TG-GGGAC--TGAA
889740 AGGTGTCCTGCTCTTTGGGGACTGAA
1 AGGTGTCCTGCTCTTTGGGGACTGAA
889766 AGGTG
1 AGGTG
889771 CCACCAACTT
Statistics
Matches: 45, Mismatches: 8, Indels: 15
0.66 0.12 0.22
Matches are distributed among these distances:
26 11 0.24
27 11 0.24
28 6 0.13
29 12 0.27
30 5 0.11
ACGTcount: A:0.17, C:0.18, G:0.36, T:0.29
Consensus pattern (26 bp):
AGGTGTCCTGCTCTTTGGGGACTGAA
Found at i:890910 original size:1 final size:1
Alignment explanation
Indices: 890892--890976 Score: 116
Period size: 1 Copynumber: 85.0 Consensus size: 1
890882 CTTAAGTAGG
* * * * * *
890892 TTTTTTCTTTTCTCTTTTTTTTTTGTTTTTTTTGTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
890957 TTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTT
890977 GAAGAGAAGG
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 72 1.00
ACGTcount: A:0.00, C:0.04, G:0.04, T:0.93
Consensus pattern (1 bp):
T
Done.