Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold353
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: 851076
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.32
Warning! 45297 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:817804 original size:3 final size:3
Alignment explanation
Indices: 817796--817820 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
817786 GAATTAAGTA
817796 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
817821 TACATAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:822605 original size:196 final size:196
Alignment explanation
Indices: 822229--822625 Score: 460
Period size: 196 Copynumber: 2.0 Consensus size: 196
822219 TCATTTTAAC
* * * *
822229 AAACGCCGCAAAAGATCAAGCATTAGGGGCGCTTATAGAAAAACGCCGCAAAAAAGTTGGGCAAA
1 AAACGCCGCAAAAGATCAAACATTAGCGGCGCTTACAGAAAAACGCCGCAAAAAAGTTGAGCAAA
* * * * *
822294 ACGACGCCATTTTCTTTTTTGAGCTTTGGTGCCATTAGCGGCACTTTTTAACAAACGCCACAAAA
66 ACGACACCACTCTCTATTTTGAGCTTTAGTGCCATTAGCGGCACTTTTTAACAAACGCCACAAAA
* ** ** * * * *
822359 AAATTAGAATTAGCGGTGCTTTTTTAAAATGCCGCTAAAGATCGAGCATTAGCGGCGCCTCTTGT
131 AAATGAGAATTAGCGACGCTTTTAAAAAACGCAGCTAAAGATCAAGCATTAGCGGCGCCTCTTGG
822424 A
196 A
* *
822425 AAACGCCGCTAAAGGTCAAACATTAGCGGCGCATTACAG-AAAACGCCGCAAAAAAGTTGAG-AA
1 AAACGCCGCAAAAGATCAAACATTAGCGGCGC-TTACAGAAAAACGCCGCAAAAAAGTTGAGCAA
* * * * * *
822488 AATGACATCGCTCTCTATTTTGAGCTTTAGTAG-TATTAGCGGCGCTTTTTAACAAACGCCGC-A
65 AACGACACCACTCTCTATTTTGAGCTTTAGT-GCCATTAGCGGCACTTTTTAACAAACGCCACAA
* * * *
822551 ATAGATCGAGAATTAGCGACGCTTTCTAAAAAACGCAGCTATAGATCAAGCATTAGCGGCGCCTT
129 AAAAAT-GAGAATTAGCGACGCTTT-TAAAAAACGCAGCTAAAGATCAAGCATTAGCGGCGCCTC
822616 TTGGA
192 TTGGA
822621 AAACG
1 AAACG
822626 TCACAAAAAA
Statistics
Matches: 167, Mismatches: 30, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
194 5 0.03
195 66 0.40
196 91 0.54
197 5 0.03
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (196 bp):
AAACGCCGCAAAAGATCAAACATTAGCGGCGCTTACAGAAAAACGCCGCAAAAAAGTTGAGCAAA
ACGACACCACTCTCTATTTTGAGCTTTAGTGCCATTAGCGGCACTTTTTAACAAACGCCACAAAA
AAATGAGAATTAGCGACGCTTTTAAAAAACGCAGCTAAAGATCAAGCATTAGCGGCGCCTCTTGG
A
Found at i:822625 original size:40 final size:39
Alignment explanation
Indices: 822522--822617 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 39
822512 CTTTAGTAGT
* * *
822522 ATTAGCGGCGCTTTTTAACAAACGCCGCAATAGATCGAGA
1 ATTAGCGGCGC-TTTTAAAAAACGCAGCAATAGATCAAGA
* * *
822562 ATTAGCGACGCTTTCTAAAAAACGCAGCTATAGATCAAGC
1 ATTAGCGGCGCTTT-TAAAAAACGCAGCAATAGATCAAGA
822602 ATTAGCGGCGCCTTTT
1 ATTAGCGGCG-CTTTT
822618 GGAAAACGTC
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
39 3 0.06
40 40 0.85
41 4 0.09
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (39 bp):
ATTAGCGGCGCTTTTAAAAAACGCAGCAATAGATCAAGA
Found at i:823464 original size:9 final size:9
Alignment explanation
Indices: 823447--823799 Score: 203
Period size: 9 Copynumber: 39.7 Consensus size: 9
823437 TTACATTTCA
823447 AACTTACAT
1 AACTTACAT
*
823456 AATTTACAT
1 AACTTACAT
* *
823465 AA-ATATAT
1 AACTTACAT
* * *
823473 ATCATATCAA
1 AACTTA-CAT
823483 AACTTACAT
1 AACTTACAT
823492 AACTTACAT
1 AACTTACAT
*
823501 AATTTACAT
1 AACTTACAT
* *
823510 AACTTTAAAG
1 AAC-TTACAT
* * * *
823520 AAATAAAAAA
1 AACT-TACAT
823530 AACTTACAT
1 AACTTACAT
823539 AACTTACAT
1 AACTTACAT
*
823548 AATTTACAT
1 AACTTACAT
823557 AACTTACAT
1 AACTTACAT
823566 AA--TACAT
1 AACTTACAT
* *
823573 AAATATATAT
1 AACT-TACAT
* *
823583 ATCATATCAT
1 AACTTA-CAT
823593 AACTTACAT
1 AACTTACAT
**
823602 AACTTATTT
1 AACTTACAT
823611 ATACTTACAT
1 A-ACTTACAT
*
823621 AA--TACGT
1 AACTTACAT
823628 AACTTACAT
1 AACTTACAT
823637 AA-TCTACAT
1 AACT-TACAT
823646 AACTTACAT
1 AACTTACAT
*
823655 AACTTATAT
1 AACTTACAT
823664 AA--TACAT
1 AACTTACAT
*
823671 AA---ATAT
1 AACTTACAT
823677 AACTTACAT
1 AACTTACAT
*
823686 AAGTTACAT
1 AACTTACAT
* *
823695 AA-ATATAT
1 AACTTACAT
* * *
823703 ATCATATCAA
1 AACTTA-CAT
823713 AACTTACAT
1 AACTTACAT
*
823722 AATTTACAT
1 AACTTACAT
*
823731 AACTCACAT
1 AACTTACAT
823740 AACTTACAT
1 AACTTACAT
823749 AACTTACAT
1 AACTTACAT
823758 AA--TACAT
1 AACTTACAT
* *
823765 AAATATATAT
1 AACT-TACAT
* *
823775 ATCATATCAT
1 AACTTA-CAT
823785 AACTTACAT
1 AACTTACAT
823794 AACTTA
1 AACTTA
823800 TTTATACTTA
Statistics
Matches: 263, Mismatches: 59, Indels: 44
0.72 0.16 0.12
Matches are distributed among these distances:
6 5 0.02
7 26 0.10
8 11 0.04
9 169 0.64
10 52 0.20
ACGTcount: A:0.48, C:0.16, G:0.01, T:0.35
Consensus pattern (9 bp):
AACTTACAT
Found at i:823623 original size:120 final size:118
Alignment explanation
Indices: 823483--823753 Score: 291
Period size: 120 Copynumber: 2.3 Consensus size: 118
823473 ATCATATCAA
823483 AACTTACATAACTTACATAATTTACATAACTTTAAAGAAATAAAAAAAACTTACATAACTTACAT
1 AACTTACATAACTTACATAA-TTACATAACTTTAAA-AAATAAAAAAAACTTACATAACTTACAT
* *
823548 AAT-T-TACATAACTTACATAA-TACATAAATATATATATCATATCATAACTTACAT
64 AATATAAACATAACTTACATAAGTACAT-AA-ATATATATCATATCAAAACTTACAT
** * * * ** * * *
823602 AACTTATTTATACTTACATAA-TACGTAAC-TTACATAATCTACATAACTTACATAACTTATATA
1 AACTTACATA-ACTTACATAATTACATAACTTTAAAAAATAAAAAAAACTTACATAACTTACATA
*
823665 ATACATAAATATAACTTACATAAGTTACATAAATATATATCATATCAAAACTTACAT
65 AT--ATAAACATAACTTACATAAG-TACATAAATATATATCATATCAAAACTTACAT
* *
823722 AATTTACATAACTCACATAACTTACATAACTT
1 AACTTACATAACTTACATAA-TTACATAACTT
823754 ACATAATACA
Statistics
Matches: 124, Mismatches: 18, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
116 25 0.20
117 4 0.03
118 7 0.06
119 18 0.15
120 55 0.44
121 9 0.07
122 6 0.05
ACGTcount: A:0.48, C:0.16, G:0.01, T:0.35
Consensus pattern (118 bp):
AACTTACATAACTTACATAATTACATAACTTTAAAAAATAAAAAAAACTTACATAACTTACATAA
TATAAACATAACTTACATAAGTACATAAATATATATCATATCAAAACTTACAT
Found at i:823659 original size:98 final size:99
Alignment explanation
Indices: 823530--823810 Score: 373
Period size: 94 Copynumber: 2.9 Consensus size: 99
823520 AAATAAAAAA
*
823530 AACTTACATAACTTACATAATTTACATAACTTACATAATACATAAATATATATATCATATCATAA
1 AACTTACATAAC-TACATAACTTACATAACTTACATAATACATAAATATATATATCATATCATAA
* *
823595 CTTACATAACTTATTTATACTTA-CATAA-TACGT
65 CTTACATAACTTATTTATACTTATCAAAACTACAT
* *
823628 AACTTACATAATCTACATAACTTACATAACTTATATAATACAT-AA-ATATA-A-CTTA-CATAA
1 AACTTACATAA-CTACATAACTTACATAACTTACATAATACATAAATATATATATCATATCATAA
* * * *
823688 GTTACATAA-ATATATAT-CATATCAAAACTTACAT
65 CTTACATAACTTATTTATACTTATCAAAAC-TACAT
*
823722 AATTTACATAACTCACATAACTTACATAACTTACATAATACATAAATATATATATCATATCATAA
1 AACTTACATAACT-ACATAACTTACATAACTTACATAATACATAAATATATATATCATATCATAA
823787 CTTACATAACTTATTTATACTTAT
65 CTTACATAACTTATTTATACTTAT
823811 AAATAAACAA
Statistics
Matches: 155, Mismatches: 16, Indels: 21
0.81 0.08 0.11
Matches are distributed among these distances:
91 3 0.02
92 10 0.06
93 15 0.10
94 45 0.29
95 3 0.02
96 10 0.06
97 3 0.02
98 42 0.27
99 14 0.09
100 6 0.04
101 4 0.03
ACGTcount: A:0.46, C:0.16, G:0.01, T:0.37
Consensus pattern (99 bp):
AACTTACATAACTACATAACTTACATAACTTACATAATACATAAATATATATATCATATCATAAC
TTACATAACTTATTTATACTTATCAAAACTACAT
Found at i:823681 original size:22 final size:23
Alignment explanation
Indices: 823653--823701 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
823643 CATAACTTAC
*
823653 ATAACTTATATAA-TACATAAAT
1 ATAACTTACATAAGTACATAAAT
823675 ATAACTTACATAAGTTACATAAAT
1 ATAACTTACATAAG-TACATAAAT
823699 ATA
1 ATA
823702 TATCATATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 12 0.50
24 12 0.50
ACGTcount: A:0.53, C:0.10, G:0.02, T:0.35
Consensus pattern (23 bp):
ATAACTTACATAAGTACATAAAT
Found at i:825122 original size:43 final size:43
Alignment explanation
Indices: 825069--825240 Score: 184
Period size: 43 Copynumber: 4.0 Consensus size: 43
825059 GGAGAGAAAC
* *
825069 GTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGTTAAAG
1 GTCATCTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGATAAAG
*** * * * * *
825112 GTCATCTTCTTTAATAGTGATTGTGATAGAAGCGCTGCTAAAG
1 GTCATCTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGATAAAG
* * * *
825155 GTCATGTTCTTTAGCGGCGTTTGTGGTAAAAGCGTCGATAAAA
1 GTCATCTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGATAAAG
* *
825198 GTCATGCTT-TTTAGCGGCATTTGTGATAAAAGCGCCGGTAAAG
1 GTCAT-CTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGATAAAG
825241 AACATGGCCT
Statistics
Matches: 101, Mismatches: 27, Indels: 2
0.78 0.21 0.02
Matches are distributed among these distances:
43 99 0.98
44 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.33
Consensus pattern (43 bp):
GTCATCTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGATAAAG
Found at i:825222 original size:86 final size:86
Alignment explanation
Indices: 825069--825232 Score: 217
Period size: 86 Copynumber: 1.9 Consensus size: 86
825059 GGAGAGAAAC
* * *
825069 GTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGTTAAAGGTCATCTTCTTTAATAGTGATT
1 GTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGATAAAAGTCATCTTCTTTAAGAGTGATT
*
825134 GTGATAGAAGCGCTGCTAAAG
66 GTGATAAAAGCGCTGCTAAAG
* * *
825155 GTCATGTTCTTTAGCGGCGTTTGTGGTAAAAGCGTCGATAAAAGTCATGCTT-TTT-AGCG-GCA
1 GTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGATAAAAGTCAT-CTTCTTTAAGAGTG-A
825217 TTTGTGATAAAAGCGC
64 -TTGTGATAAAAGCGC
825233 CGGTAAAGAA
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
84 1 0.01
85 3 0.04
86 61 0.90
87 3 0.04
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (86 bp):
GTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGATAAAAGTCATCTTCTTTAAGAGTGATT
GTGATAAAAGCGCTGCTAAAG
Found at i:834369 original size:294 final size:288
Alignment explanation
Indices: 833846--834383 Score: 801
Period size: 294 Copynumber: 1.8 Consensus size: 288
833836 AATCTAGTAT
* * * *
833846 ATTGATAATATTGTTGGTTGAGTTGGTGTCATAAGCTAACTCAACAGTAACTCAAGATTCATGAT
1 ATTGATAATATGGTTGATTGAGTTGGTGTCACAAACTAACTCAACAGTAACTCAAGATTCATGAT
* * *
833911 AAACAATTTTTGTTCATTTAATATTCTTAATTTGATGTATTTAAATTTTATTTTGCTCACAATTT
66 AAACAATTTTTGTACATTCAATATTCTTAATTTGATGTATTTAAATTTTATTTTACTCACAATTT
* * *
833976 AATCTACTTTTTCATTTTAATATCATATATATTTAATGTGTTATTATTAATCAATTTCAAACCAT
131 AATCTACTTTTTCATTTTAATATCATACATACTTAATATGTTATTATTAATCAATTTCAAACCAT
834041 AAGTTTCATTATATCATATGTTATTTTTAAATACCCCTATGTGTTCTAAATACGTAGTTTCCACG
196 AAGTTTCATTATATCATATGTTATTTTTAAATACCCCTATGTGTTCTAAATACGTAGTTTCCACG
834106 TGCATACACGAATGATAGAATTTTTAGC
261 TGCATACACGAATGATAGAATTTTTAGC
* * * *
834134 ATTGATAATGTGGTTGATTGAGTTGGTGTCACAAACTAAGTCAATATTAACTCAAGATTCATGAT
1 ATTGATAATATGGTTGATTGAGTTGGTGTCACAAACTAACTCAACAGTAACTCAAGATTCATGAT
* *
834199 AAACAATTTTTGTACATTCAGTATTCTTAATTTGAAGTATTTACGTATTTAAATTTTGTTTTACT
66 AAACAATTTTTGTACATTCAATATTCTTAATTT---G-A--T--GTATTTAAATTTTATTTTACT
* * *
834264 CACAATTT-ATTTA-TTTTTCATTTTAATATCATACATACTTCATATGTTATTATTAATTAATTT
123 CACAATTTAATCTACTTTTTCATTTTAATATCATACATACTTAATATGTTATTATTAATCAATTT
* *
834327 CAAACCATACGTTTTATTATATCATATGTTATTTTTAAATACCCCTATGTGTTCTAA
188 CAAACCATAAGTTTCATTATATCATATGTTATTTTTAAATACCCCTATGTGTTCTAA
834384 GTACATAAAG
Statistics
Matches: 221, Mismatches: 21, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
288 87 0.39
291 1 0.00
292 1 0.00
294 101 0.46
295 4 0.02
296 27 0.12
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.45
Consensus pattern (288 bp):
ATTGATAATATGGTTGATTGAGTTGGTGTCACAAACTAACTCAACAGTAACTCAAGATTCATGAT
AAACAATTTTTGTACATTCAATATTCTTAATTTGATGTATTTAAATTTTATTTTACTCACAATTT
AATCTACTTTTTCATTTTAATATCATACATACTTAATATGTTATTATTAATCAATTTCAAACCAT
AAGTTTCATTATATCATATGTTATTTTTAAATACCCCTATGTGTTCTAAATACGTAGTTTCCACG
TGCATACACGAATGATAGAATTTTTAGC
Found at i:835301 original size:11 final size:11
Alignment explanation
Indices: 835287--835324 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
835277 CAATATCCTT
835287 TCAAATTTCTC
1 TCAAATTTCTC
835298 TCAAATTTCTC
1 TCAAATTTCTC
* *
835309 TTAAATTCCTC
1 TCAAATTTCTC
835320 TCAAA
1 TCAAA
835325 GCTCTCTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.42
Consensus pattern (11 bp):
TCAAATTTCTC
Found at i:835314 original size:22 final size:22
Alignment explanation
Indices: 835289--835338 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
835279 ATATCCTTTC
**
835289 AAATTTCTCTCAAATTTCTCTT
1 AAATTTCTCTCAAAGCTCTCTT
*
835311 AAATTCCTCTCAAAGCTCTCTT
1 AAATTTCTCTCAAAGCTCTCTT
*
835333 TAATTT
1 AAATTT
835339 TTTTTCGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.28, C:0.24, G:0.02, T:0.46
Consensus pattern (22 bp):
AAATTTCTCTCAAAGCTCTCTT
Found at i:836418 original size:11 final size:11
Alignment explanation
Indices: 836404--836431 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
836394 AAGAGAGCTC
836404 TGAGAGAAATT
1 TGAGAGAAATT
836415 TGAGAGAAATT
1 TGAGAGAAATT
836426 TGAGAG
1 TGAGAG
836432 GATATTGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.32, T:0.25
Consensus pattern (11 bp):
TGAGAGAAATT
Found at i:839645 original size:11 final size:11
Alignment explanation
Indices: 839629--839655 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
839619 CCCATTTTTC
839629 TATTTTTAACT
1 TATTTTTAACT
839640 TATTTTTAACT
1 TATTTTTAACT
839651 TATTT
1 TATTT
839656 GATCCCATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (11 bp):
TATTTTTAACT
Found at i:842174 original size:17 final size:17
Alignment explanation
Indices: 842137--842184 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
842127 GAATTTAGAA
*
842137 GAATTTT-TGAATTAGT
1 GAATTTTGTGATTTAGT
*
842153 GAATTTTGTGATTTATT
1 GAATTTTGTGATTTAGT
842170 GAATTTTGTGATTTA
1 GAATTTTGTGATTTA
842185 AAAAGAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (17 bp):
GAATTTTGTGATTTAGT
Found at i:843955 original size:24 final size:24
Alignment explanation
Indices: 843923--843972 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
843913 TTCATATGGC
843923 TGAACTTTTATGATTAATTGTTAA
1 TGAACTTTTATGATTAATTGTTAA
843947 TGAACTTTTATGATTAATTGTTAA
1 TGAACTTTTATGATTAATTGTTAA
843971 TG
1 TG
843973 TGGGAATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.32, C:0.04, G:0.14, T:0.50
Consensus pattern (24 bp):
TGAACTTTTATGATTAATTGTTAA
Found at i:844214 original size:46 final size:45
Alignment explanation
Indices: 844143--844329 Score: 259
Period size: 46 Copynumber: 4.1 Consensus size: 45
844133 TCCATGGAAA
* *
844143 AGTT-TGAAACGTAGGTATGGTATTTCAGTGAATAAAACCATACTG
1 AGTTGTGAAAAGTAGGTATGGTATTTC-GTGAAGAAAACCATACTG
* *
844188 AGTTGTGAAAAGTAGGTATGGTATTTCGATAAAGAAAACCATATTG
1 AGTTGTGAAAAGTAGGTATGGTATTTCG-TGAAGAAAACCATACTG
* *
844234 AGTTGTGAAAAGTAGGTATGATGTTTCAGTGAAGAAAACCATACTG
1 AGTTGTGAAAAGTAGGTATGGTATTTC-GTGAAGAAAACCATACTG
**
844280 AGTTACGAAAAGTAGGTATGGTATTTTCGTGAAGAAAACCATACTG
1 AGTTGTGAAAAGTAGGTATGGTA-TTTCGTGAAGAAAACCATACTG
844326 AGTT
1 AGTT
844330 ATAGCAATGT
Statistics
Matches: 126, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
45 5 0.04
46 116 0.92
47 5 0.04
ACGTcount: A:0.37, C:0.09, G:0.24, T:0.30
Consensus pattern (45 bp):
AGTTGTGAAAAGTAGGTATGGTATTTCGTGAAGAAAACCATACTG
Found at i:845697 original size:416 final size:416
Alignment explanation
Indices: 844868--845700 Score: 1386
Period size: 416 Copynumber: 2.0 Consensus size: 416
844858 TAAATGAAGT
* *
844868 AGTTGAAATACCGAAATTGGTTGTGAATTGAAATTTGCAGGGAAGGTTAGATAATTATAAAGGGG
1 AGTTGAAATAACGAAATTGGTTGTGAATTGAAATTTGCAGGGAAGGTTAAATAATTATAAAGGGG
*
844933 TTATATTGAATTTTTTTTAAAAAAATAAAATAAAATTGCAATGGAACAGTTTTTGGACAACAGCA
66 TTATATTGAATTTTTTTAAAAAAAATAAAATAAAATTGCAATGGAACAGTTTTTGGACAACAGCA
*
844998 TTGATGTAACTTTGAAAAATCACCAAAAATAGCGTAAATTGAATTAGAAGCTAAGTGAGATACGA
131 TTGATGTAACTTTGAAAAATCACCAAAAATAGCGAAAATTGAATTAGAAGCTAAGTGAGATACGA
* *
845063 AATTAAAGCTGAATGAGTCTATTTTCACATGAAAGAAATATAGTAAGCAAAAGAGTTATATATTT
196 AATTAAAGCTGAATGAGTCTACTTTCACATGAAAGAAATAGAGTAAGCAAAAGAGTTATATATTT
* * *
845128 TTAGATATTTTAATTTTAGTGAGATAGGATAAGAATGGTTTTTGAAGTCCCCTGTTCTAACTTTA
261 TTACATATTTTAATTTTAGTGAGATAGGATAAGAATAGTTTTTGAAGTCCCCTATTCTAACTTTA
* *
845193 GAAATTAATTAAAAATTTTACAGAAAGAATTATGAGTTATAATTTATATTTGTAGATTCCTTAAT
326 GAAATTAATTAAAAATTTTACAGAAAGAATTATGAGTTATAATTTATATGTATAGATTCCTTAAT
845258 GAGTCTATTTTAAGTAGAATAAGTGG
391 GAGTCTATTTTAAGTAGAATAAGTGG
*
845284 AGTTGAAATAATGAAATTGGTTGT-AATTTGAAATTTGCAGGGAAGGTTAAATAATTATAAAGGG
1 AGTTGAAATAACGAAATTGGTTGTGAA-TTGAAATTTGCAGGGAAGGTTAAATAATTATAAAGGG
*
845348 GTTATATTG-ATTTTTTTAAAAAAAAATAAAATAAAATTTCAATGGAACAGTTTTTGGACAACAG
65 GTTATATTGAATTTTTTT-AAAAAAAATAAAATAAAATTGCAATGGAACAGTTTTTGGACAACAG
* * *
845412 CATT-ATTGTAACTTTGAAAAATCACCAAAAATGGTGAAAATTGAATTAGAAGCTGAGTGAGATA
129 CATTGA-TGTAACTTTGAAAAATCACCAAAAATAGCGAAAATTGAATTAGAAGCTAAGTGAGATA
* *
845476 TGAAATTAAAGCTGAATGAGTCTACTTTCACATGAAAGAAATAGAGTAAGCAGAAGAGTTATATA
193 CGAAATTAAAGCTGAATGAGTCTACTTTCACATGAAAGAAATAGAGTAAGCAAAAGAGTTATATA
* *
845541 TTTTTACATATTTTAATTTTAGTGAGATAGG-TAAGAATATTTTTTGAAGTCCCCTATTCTGACT
258 TTTTTACATATTTTAATTTTAGTGAGATAGGATAAGAATAGTTTTTGAAGTCCCCTATTCTAACT
* * *
845605 TTAGAAATTCATTAAAAATTTTACAGAAGGAATTATGAGTTATAATTTATATGTATAGATTCTTT
323 TTAGAAATTAATTAAAAATTTTACAGAAAGAATTATGAGTTATAATTTATATGTATAGATTCCTT
*
845670 AATGAGTCTATTTTCAGTAGAAATAAGTGG
388 AATGAGTCTATTTTAAGTAG-AATAAGTGG
845700 A
1 A
845701 AGCACCATAT
Statistics
Matches: 389, Mismatches: 24, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
415 119 0.31
416 270 0.69
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (416 bp):
AGTTGAAATAACGAAATTGGTTGTGAATTGAAATTTGCAGGGAAGGTTAAATAATTATAAAGGGG
TTATATTGAATTTTTTTAAAAAAAATAAAATAAAATTGCAATGGAACAGTTTTTGGACAACAGCA
TTGATGTAACTTTGAAAAATCACCAAAAATAGCGAAAATTGAATTAGAAGCTAAGTGAGATACGA
AATTAAAGCTGAATGAGTCTACTTTCACATGAAAGAAATAGAGTAAGCAAAAGAGTTATATATTT
TTACATATTTTAATTTTAGTGAGATAGGATAAGAATAGTTTTTGAAGTCCCCTATTCTAACTTTA
GAAATTAATTAAAAATTTTACAGAAAGAATTATGAGTTATAATTTATATGTATAGATTCCTTAAT
GAGTCTATTTTAAGTAGAATAAGTGG
Done.