Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2349
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: 43140
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:1748 original size:20 final size:20
Alignment explanation
Indices: 1712--1750 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1702 AGATAACTTA
*
1712 AATTCAAAAACATAAAAAAC
1 AATTCAAAAACAAAAAAAAC
1732 AATTCAGAAAA-AAAAAAAA
1 AATTCA-AAAACAAAAAAAA
1751 AAGATACCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.74, C:0.10, G:0.03, T:0.13
Consensus pattern (20 bp):
AATTCAAAAACAAAAAAAAC
Found at i:3772 original size:28 final size:27
Alignment explanation
Indices: 3731--3792 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
3721 TTTGAAGATC
* * *
3731 CAAAAGTCTTTAAATTGGGATAAAATTT
1 CAAAAATCTCTAAATT-GAATAAAATTT
3759 CAAAAATCTCTAAATTGAATAAAATTT
1 CAAAAATCTCTAAATTGAATAAAATTT
*
3786 CATAAAT
1 CAAAAAT
3793 TTAAAAAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 16 0.53
28 14 0.47
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.34
Consensus pattern (27 bp):
CAAAAATCTCTAAATTGAATAAAATTT
Found at i:3782 original size:18 final size:18
Alignment explanation
Indices: 3760--3802 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3750 ATAAAATTTC
3760 AAAAATCTC-TAAATTGA
1 AAAAATCTCATAAATTGA
* *
3777 ATAAAATTTCATAAATTTA
1 A-AAAATCTCATAAATTGA
3796 AAAAATC
1 AAAAATC
3803 CGGAACTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 1 0.05
18 12 0.57
19 8 0.38
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (18 bp):
AAAAATCTCATAAATTGA
Found at i:4921 original size:57 final size:57
Alignment explanation
Indices: 4833--4947 Score: 212
Period size: 57 Copynumber: 2.0 Consensus size: 57
4823 TTATTTTCCC
*
4833 ACAAAAATTATGTGCTAGATAAGTTTTAATAATATTATACAAATTAAGAAGACTATA
1 ACAAAAATTATGTGCTAGATAAGTTTTAATAATATTATACAAATTAAAAAGACTATA
*
4890 ACAAAAATTATGTGCTAGATAAGTTTTAATAATATTATACAAATTAAAAAGATTATA
1 ACAAAAATTATGTGCTAGATAAGTTTTAATAATATTATACAAATTAAAAAGACTATA
4947 A
1 A
4948 TACAAATAAG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.34
Consensus pattern (57 bp):
ACAAAAATTATGTGCTAGATAAGTTTTAATAATATTATACAAATTAAAAAGACTATA
Found at i:4987 original size:16 final size:16
Alignment explanation
Indices: 4963--5012 Score: 59
Period size: 15 Copynumber: 3.1 Consensus size: 16
4953 ATAAGTGTTT
4963 TAAAATTTATATAATA
1 TAAAATTTATATAATA
*
4979 TAAATTTTA-AT-ATA
1 TAAAATTTATATAATA
4993 TTAAAATTTATATAAATA
1 -TAAAATTTATAT-AATA
5011 TA
1 TA
5013 TAATATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
14 3 0.11
15 10 0.36
16 10 0.36
17 2 0.07
18 3 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TAAAATTTATATAATA
Found at i:5012 original size:20 final size:19
Alignment explanation
Indices: 4987--5047 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
4977 TATAAATTTT
*
4987 AATATATTAAAATTTATATA
1 AATATATTAAAATTT-TAAA
*
5007 AATATA-TAATATTTTAAA
1 AATATATTAAAATTTTAAA
*
5025 AATA-ATTATAATTTTTAAA
1 AATATATTA-AAATTTTAAA
5044 AATA
1 AATA
5048 AGTGAATACA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 1 0.03
18 9 0.26
19 19 0.54
20 6 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AATATATTAAAATTTTAAA
Found at i:5038 original size:37 final size:34
Alignment explanation
Indices: 4976--5047 Score: 81
Period size: 37 Copynumber: 2.0 Consensus size: 34
4966 AATTTATATA
* *
4976 ATATAAATTTTAATATATTAAAATTTATATAAAT
1 ATATAAATTTTAAAATATTAAAATTTATAAAAAT
* *
5010 ATATAATATTTTAAAAATAATTATAATTTTTAAAAAT
1 ATATAA-ATTTT-AAAAT-ATTAAAATTTATAAAAAT
5047 A
1 A
5048 AGTGAATACA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
34 6 0.19
35 5 0.16
36 4 0.13
37 16 0.52
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (34 bp):
ATATAAATTTTAAAATATTAAAATTTATAAAAAT
Found at i:5042 original size:19 final size:20
Alignment explanation
Indices: 5011--5048 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
5001 TATATAAATA
5011 TATAATATTTTAAAAATAAT
1 TATAATATTTTAAAAATAAT
5031 TATAAT-TTTTAAAAATAA
1 TATAATATTTTAAAAATAA
5049 GTGAATACAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TATAATATTTTAAAAATAAT
Found at i:6627 original size:47 final size:47
Alignment explanation
Indices: 6546--6642 Score: 144
Period size: 47 Copynumber: 2.1 Consensus size: 47
6536 ATATTTAATG
*
6546 AATAAATATAACATATTTTAATAATATAATATTATATTTAAATTTAA
1 AATAAAAATAACATATTTTAATAATATAATATTATATTTAAATTTAA
*
6593 AATAAAAATAATATAATATTTAATAA-AT-ATATTATATTTAAATTTAA
1 AATAAAAATAACAT-AT-TTTAATAATATAATATTATATTTAAATTTAA
6640 AAT
1 AAT
6643 TTTTAAATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 34 0.74
48 4 0.09
49 8 0.17
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (47 bp):
AATAAAAATAACATATTTTAATAATATAATATTATATTTAAATTTAA
Found at i:6629 original size:18 final size:19
Alignment explanation
Indices: 6598--6633 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
6588 TTTAAAATAA
6598 AAATAATATAATATTTAAT
1 AAATAATATAATATTTAAT
*
6617 AAAT-ATATTATATTTAA
1 AAATAATATAATATTTAA
6634 ATTTAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AAATAATATAATATTTAAT
Found at i:6906 original size:47 final size:47
Alignment explanation
Indices: 6852--6979 Score: 184
Period size: 47 Copynumber: 2.7 Consensus size: 47
6842 TCATTTCAGG
* * *
6852 GTAATTTTGTAATTAAAACCAAACTGAAGGATGATGTTAATTGCTGA
1 GTAATTTTATAATTAAAACCAAACTGAGGGATGATGTTAATTGATGA
* *
6899 GTAATTTTATAATTAAAACCAAACTGAGGGATGATTTTAATTGATTA
1 GTAATTTTATAATTAAAACCAAACTGAGGGATGATGTTAATTGATGA
* * *
6946 GTAATTTTATAATAAAAAGCAAATTGAGGGATGA
1 GTAATTTTATAATTAAAACCAAACTGAGGGATGA
6980 AAAAAATATA
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 73 1.00
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.34
Consensus pattern (47 bp):
GTAATTTTATAATTAAAACCAAACTGAGGGATGATGTTAATTGATGA
Found at i:8173 original size:2 final size:2
Alignment explanation
Indices: 8166--8204 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
8156 GCGAAGCTTT
8166 TA TA TA TA TA 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 TA TA TA TA TA T
8205 TGTGCATTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9600 original size:2 final size:2
Alignment explanation
Indices: 9593--9637 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
9583 CAACATAGGT
9593 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9635 TA T
1 TA T
9638 TTTGTTAGCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10761 original size:21 final size:21
Alignment explanation
Indices: 10732--10796 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
10722 TAACTTTATA
10732 AATTATTATTATGATTAAATTT
1 AATT-TTATTATGATTAAATTT
* * * *
10754 AATTTTATTGTAACTAAGTTT
1 AATTTTATTATGATTAAATTT
* * *
10775 AATTTTAGTACGATGAAATTT
1 AATTTTATTATGATTAAATTT
10796 A
1 A
10797 TTAAGTTTTT
Statistics
Matches: 32, Mismatches: 11, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
21 28 0.88
22 4 0.12
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.49
Consensus pattern (21 bp):
AATTTTATTATGATTAAATTT
Found at i:13305 original size:88 final size:90
Alignment explanation
Indices: 13192--13882 Score: 538
Period size: 91 Copynumber: 7.7 Consensus size: 90
13182 CGTGAAATTC
* * * * * * *
13192 GAAATATGTGAAAGATGCAAGGGGTATCAGATTTTTTCTAACACAACAGAAAATATTTTATTAAT
1 GAAATATGTGACAGATGCATGGGGTATCAGATTTCTTCTGACACGACAAAAAATATTTGATTAAT
13257 GCCTAATAAA-TT-TCTTGAAACCT
66 GCCTAATAAATTTATCTTGAAACCT
* * * * * * * * *
13280 GAAATATGTGACACATGTATGGGGTATTAGATTTCTACTAACACAACATAAAATATTCGACTAAT
1 GAAATATGTGACAGATGCATGGGGTATCAGATTTCTTCTGACACGACAAAAAATATTTGATTAAT
* * *
13345 ACATAATAAATTTAATCTTGGAA-CT
66 GCCTAATAAATTT-ATCTTGAAACCT
* * * * * *
13370 CGGAAGATGTGACAGATGCATGAGGTATCAG-TTTCTACTGACACGATAAAAAATATTTGACTAA
1 -GAAATATGTGACAGATGCATGGGGTATCAGATTTCTTCTGACACGACAAAAAATATTTGATTAA
* **
13434 TACCTAATAAATTT-T-TTGAAATTT
65 TGCCTAATAAATTTATCTTGAAACCT
* * * *
13458 GAAATATGTTAAAGATGCATGGGGTATCAGATGCTT-TT-TGATACGACAGAAAATATTTGATTA
1 GAAATATGTGACAGATGCATGGGGTATCAGAT--TTCTTCTGACACGACAAAAAATATTTGATTA
13521 ATGCCTAATAAATTTAATCTTTG-AACCT
64 ATGCCTAATAAATTT-ATC-TTGAAACCT
* * * *
13549 AAAATATGTGACAGATGCATGGGGTATCAGATTCCTTATGGATACGACAAAAAATATTTGATTAA
1 GAAATATGTGACAGATGCATGGGGTATCAGATTTCTTCT-GACACGACAAAAAATATTTGATTAA
*
13614 TGCCTAATAAATTTAATCTTGAAAACT
65 TGCCTAATAAATTT-ATCTTGAAACCT
* * * * * * *
13641 GAAAGATGT-ACAGATGCATGGGGCATCAGATTCCTTATGATA-G----AAAATATTTGACTAGT
1 GAAATATGTGACAGATGCATGGGGTATCAGATTTCTTCTGACACGACAAAAAATATTTGATTAAT
* *
13700 GCCTCATAAATTTAATTTTGAAA-CT
66 GCCTAATAAATTT-ATCTTGAAACCT
* * * * * * * *
13725 CGAAAGATGTGACAAAT-CTATGGGGTATCAGATTCCTTTTGATACGACAGAAAATATTTAACTA
1 -GAAATATGTGACAGATGC-ATGGGGTATCAGATTTCTTCTGACACGACAAAAAATATTTGATTA
*
13789 ATGCCTAATAAATTTAAT-TTTAGAACCT
64 ATGCCTAATAAATTT-ATCTTGA-AACCT
* * * ** * * * * *
13817 AAAAGATGTGATAGATGCATGCTGTATCAGA-TTCTTTCTAACATGACAGAAAAGATTTGACTAA
1 GAAATATGTGACAGATGCATGGGGTATCAGATTTC-TTCTGACACGACAAAAAATATTTGATTAA
13881 TG
65 TG
13883 ACACGATAGA
Statistics
Matches: 502, Mismatches: 73, Indels: 53
0.80 0.12 0.08
Matches are distributed among these distances:
84 2 0.00
85 45 0.09
86 28 0.06
87 31 0.06
88 100 0.20
89 5 0.01
90 57 0.11
91 175 0.35
92 59 0.12
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (90 bp):
GAAATATGTGACAGATGCATGGGGTATCAGATTTCTTCTGACACGACAAAAAATATTTGATTAAT
GCCTAATAAATTTATCTTGAAACCT
Found at i:13737 original size:177 final size:178
Alignment explanation
Indices: 13168--13837 Score: 563
Period size: 178 Copynumber: 3.8 Consensus size: 178
13158 ATAACGTGTT
* ** * * * * ** * *
13168 CTAATAAAATTAATCGTGAAATTCGAAATATGTGAAAGATGCAAGGGGTATCAGATTTTTTCTAA
1 CTAATAAATTTAATTTTGAAACTCGAAAGATGTGACAGATGCATGGGGTATCAGATTCCTTATGA
* * * * * * * * * *
13233 CACAACAGAAAATATTTTATTAATGCCTAATAAATTT--CTTGAAACCTGAAATATGTGACACAT
66 TACGACAAAAAATATTTGACTAATGCCTAATAAATTTAATTTGAAAACTGAAAGATGT-AAAGAT
* * * * * * * * * *
13296 GTATGGGGTATTAGAT-TTCTACTAACACAACATAAAATATTCGACTAATAC
130 GCATGGGGCATCAGATCTCCT--TGATA-GACAGAAAATATTTGACTAATGC
* * * * * *
13347 ATAATAAATTTAATCTTGGAACTCGGAAGATGTGACAGATGCATGAGGTATCAG-TTTC-TACTG
1 CTAATAAATTTAATTTTGAAACTCGAAAGATGTGACAGATGCATGGGGTATCAGATTCCTTA-TG
* * * ** *
13410 ACACGATAAAAAATATTTGACTAATACCTAATAAATTT--TTTGAAATTTGAAATATGTTAAAGA
65 ATACGACAAAAAATATTTGACTAATGCCTAATAAATTTAATTTGAAAACTGAAAGATG-TAAAGA
* ** *
13473 TGCATGGGGTATCAGATGCTTTTTGATACGACAGAAAATATTTGATTAATGC
129 TGCATGGGGCATCAGAT-CTCCTTGATA-GACAGAAAATATTTGACTAATGC
* * *
13525 CTAATAAATTTAATCTTTGAACCT-AAAATATGTGACAGATGCATGGGGTATCAGATTCCTTATG
1 CTAATAAATTTAAT-TTTGAAACTCGAAAGATGTGACAGATGCATGGGGTATCAGATTCCTTAT-
* *
13589 GATACGACAAAAAATATTTGATTAATGCCTAATAAATTTAATCTTGAAAACTGAAAGATGTACAG
64 GATACGACAAAAAATATTTGACTAATGCCTAATAAATTTAAT-TTGAAAACTGAAAGATGTAAAG
* *
13654 ATGCATGGGGCATCAGAT-TCCTT-AT-GATAGAAAATATTTGACTAGTGC
128 ATGCATGGGGCATCAGATCTCCTTGATAGACAGAAAATATTTGACTAATGC
* * *
13702 CTCATAAATTTAATTTTGAAACTCGAAAGATGTGACAAAT-CTATGGGGTATCAGATTCCTTTTG
1 CTAATAAATTTAATTTTGAAACTCGAAAGATGTGACAGATGC-ATGGGGTATCAGATTCCTTATG
* * * * * *
13766 ATACGACAGAAAATATTTAACTAATGCCTAATAAATTTAATTTTAGAACCTAAAAGATGTGATAG
65 ATACGACAAAAAATATTTGACTAATGCCTAATAAATTTAATTTGA-AAACTGAAAGATGT-AAAG
13831 ATGCATG
128 ATGCATG
13838 CTGTATCAGA
Statistics
Matches: 406, Mismatches: 70, Indels: 32
0.80 0.14 0.06
Matches are distributed among these distances:
175 3 0.01
176 60 0.15
177 77 0.19
178 130 0.32
179 57 0.14
180 43 0.11
182 22 0.05
183 14 0.03
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (178 bp):
CTAATAAATTTAATTTTGAAACTCGAAAGATGTGACAGATGCATGGGGTATCAGATTCCTTATGA
TACGACAAAAAATATTTGACTAATGCCTAATAAATTTAATTTGAAAACTGAAAGATGTAAAGATG
CATGGGGCATCAGATCTCCTTGATAGACAGAAAATATTTGACTAATGC
Found at i:13770 original size:268 final size:267
Alignment explanation
Indices: 13184--13859 Score: 721
Period size: 268 Copynumber: 2.5 Consensus size: 267
13174 AAATTAATCG
* * * ** * * *
13184 TGAAATTCGAAATATGTGAAAGATGCAAGGGGTATCAGAT-TTTTTCTAACACAACAGAAAATAT
1 TGAAACTCGAAAGATGTGAAAGATGCATGGGGTATCAGATGCCTTT-TGATACGACAGAAAATAT
* * * * *
13248 TTTATTAATGCCTAATAAA-TT--TC-TTGAAACCTGAAATATGTGACACATGTATGGGGTATTA
65 TTAATTAATGCCTAATAAATTTAATCTTTG-AACCTAAAATATGTGACAGATGCATGGGGTATCA
* * * *
13309 GATTTCTACTAACACAACATAAAATATTCGACTAATACATAATAAATTTAATCTTGGAACTCGGA
129 GATTCCTACTAACACAACAAAAAATATTCGACTAATACATAATAAATTTAATCTTGAAACTCGAA
* *
13374 AGATGTGACAGATGCATGAGGTATCAGTTTCTACTGACACGATAAAAAATATTTGACTAATACCT
194 AGATGTGACAGATGCATGAGGCATCAGATTC-ACT-ACACGATAAAAAATATTTGACTAATACCT
13439 AATAAATTTTT
257 AATAAATTTTT
* * * * *
13450 TGAAATTTGAAATATGTTAAAGATGCATGGGGTATCAGATGCTTTTTGATACGACAGAAAATATT
1 TGAAACTCGAAAGATGTGAAAGATGCATGGGGTATCAGATGCCTTTTGATACGACAGAAAATATT
*
13515 TGATTAATGCCTAATAAATTTAATCTTTGAACCTAAAATATGTGACAGATGCATGGGGTATCAGA
66 TAATTAATGCCTAATAAATTTAATCTTTGAACCTAAAATATGTGACAGATGCATGGGGTATCAGA
* * * * * * *
13580 TTCCTTA-TGGATACGACAAAAAATATTTGATTAATGCCTAATAAATTTAATCTTGAAAACT-GA
131 TTCC-TACT-AACACAACAAAAAATATTCGACTAATACATAATAAATTTAATCTTG-AAACTCGA
* * * * * * *
13643 AAGATGT-ACAGATGCATGGGGCATCAGATTC-CT-TATGATAGAAAATATTTGACTAGTGCCTC
193 AAGATGTGACAGATGCATGAGGCATCAGATTCACTACACGATAAAAAATATTTGACTAATACCTA
13705 ATAAATTTAATTT
258 ATAAA-TT--TTT
*
13718 TGAAACTCGAAAGATGTGACAA-AT-CTATGGGGTATCAGATTCCTTTTGATACGACAGAAAATA
1 TGAAACTCGAAAGATGTGA-AAGATGC-ATGGGGTATCAGATGCCTTTTGATACGACAGAAAATA
* * * **
13781 TTTAACTAATGCCTAATAAATTTAAT-TTTAGAACCTAAAAGATGTGATAGATGCATGCTGTATC
64 TTTAATTAATGCCTAATAAATTTAATCTTT-GAACCTAAAATATGTGACAGATGCATGGGGTATC
* *
13845 AGATTCTTTCTAACA
128 AGATTCCTACTAACA
13860 TGACAGAAAA
Statistics
Matches: 347, Mismatches: 48, Indels: 29
0.82 0.11 0.07
Matches are distributed among these distances:
265 28 0.08
266 72 0.21
267 15 0.04
268 116 0.33
269 61 0.18
270 51 0.15
271 4 0.01
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (267 bp):
TGAAACTCGAAAGATGTGAAAGATGCATGGGGTATCAGATGCCTTTTGATACGACAGAAAATATT
TAATTAATGCCTAATAAATTTAATCTTTGAACCTAAAATATGTGACAGATGCATGGGGTATCAGA
TTCCTACTAACACAACAAAAAATATTCGACTAATACATAATAAATTTAATCTTGAAACTCGAAAG
ATGTGACAGATGCATGAGGCATCAGATTCACTACACGATAAAAAATATTTGACTAATACCTAATA
AATTTTT
Found at i:13848 original size:177 final size:177
Alignment explanation
Indices: 13329--13850 Score: 490
Period size: 177 Copynumber: 2.9 Consensus size: 177
13319 AACACAACAT
* * * * ** * *
13329 AAAATATTCGACTAATACATAATAAATTTAATC-TTGGAACTCGGAAGATGTGACAGATGCATGA
1 AAAATATTTGACTAATGCCTAATAAATTTAATCTTTGAAACT-AAAAGATGTGACAAATGCATGG
* * * * *
13393 GGTATCAG-TTTC-TACT-GACACGATAAAAAATATTTGACTAATACCTAATAAATTT--T-TTG
65 GGTATCAGATTCCTTA-TGGATACGACAAAAAATATTTAACTAATGCCTAATAAATTTAATCTTG
** * * * * * ** *
13452 AAATTTGAAATATGTTAAAGATGCATGGGGTATCAGATGCTTTTTGATACGACAG
129 AAAACTAAAAGATG-TACAGATGCATGCGGCATCAGAT--TCCTT-AT--GATAG
* * * *
13507 AAAATATTTGATTAATGCCTAATAAATTTAATCTTTGAACCTAAAATATGTGACAGATGCATGGG
1 AAAATATTTGACTAATGCCTAATAAATTTAATCTTTGAAACTAAAAGATGTGACAAATGCATGGG
* *
13572 GTATCAGATTCCTTATGGATACGACAAAAAATATTTGATTAATGCCTAATAAATTTAATCTTGAA
66 GTATCAGATTCCTTATGGATACGACAAAAAATATTTAACTAATGCCTAATAAATTTAATCTTGAA
* *
13637 AACTGAAAGATGTACAGATGCATGGGGCATCAGATTCCTTATGATAG
131 AACTAAAAGATGTACAGATGCATGCGGCATCAGATTCCTTATGATAG
* * *
13684 AAAATATTTGACTAGTGCCTCATAAATTTAAT-TTTGAAACTCGAAAGATGTGACAAAT-CTATG
1 AAAATATTTGACTAATGCCTAATAAATTTAATCTTTGAAACT-AAAAGATGTGACAAATGC-ATG
* * *
13747 GGGTATCAGATTCCTT-TTGATACGACAGAAAATATTTAACTAATGCCTAATAAATTTAAT-TTT
64 GGGTATCAGATTCCTTATGGATACGACAAAAAATATTTAACTAATGCCTAATAAATTTAATCTTG
* * * *
13810 AGAACCTAAAAGATGTGATAGATGCATGCTGTATCAGATTC
129 A-AAACTAAAAGATGT-ACAGATGCATGCGGCATCAGATTC
13851 TTTCTAACAT
Statistics
Matches: 292, Mismatches: 41, Indels: 23
0.82 0.12 0.06
Matches are distributed among these distances:
175 3 0.01
176 61 0.21
177 85 0.29
178 55 0.19
179 12 0.04
180 40 0.14
182 22 0.08
183 14 0.05
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (177 bp):
AAAATATTTGACTAATGCCTAATAAATTTAATCTTTGAAACTAAAAGATGTGACAAATGCATGGG
GTATCAGATTCCTTATGGATACGACAAAAAATATTTAACTAATGCCTAATAAATTTAATCTTGAA
AACTAAAAGATGTACAGATGCATGCGGCATCAGATTCCTTATGATAG
Found at i:21862 original size:20 final size:20
Alignment explanation
Indices: 21839--21876 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
21829 AAAGTACTCA
21839 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTCTTC
*
21859 AATGTATCGATATATTCT
1 AATGTATCGATACATTCT
21877 ATCTTTCTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (20 bp):
AATGTATCGATACATTCTTC
Found at i:37087 original size:28 final size:28
Alignment explanation
Indices: 37047--37443 Score: 382
Period size: 28 Copynumber: 13.6 Consensus size: 28
37037 CGTTCATCTC
*
37047 TTCAAAGTCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * * *
37075 TTCAAAGCCCACAAGTCAATCGCATCAT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
37103 TTCAAAGCCCACTCAAGTCGGTGGCAACTCAT
1 TTCAAAGCCCA--CAAGTCAGTGGC-AC-CCT
* * *
37135 TTGAAAGCCCACACAAGTCAGTGGCATCAT
1 TTCAAAG-CC-CACAAGTCAGTGGCACCCT
* * *
37165 TTCAAAGCCTGCACAAGTCGGTGACAACTCAT
1 TTCAAAGCC--CACAAGTCAGTGGC-AC-CCT
*
37197 TTCAAAGCCCACACAAGT-TGATGGCAACCCAT
1 TTCAAAG-CC-CACAAGTCAG-TGGC-ACCC-T
* * *
37229 TTCATAGCCCATAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
37257 TTCAAAGCCCACAAATTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
*
37286 TTCAAAACCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
37314 TTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* *
37343 TTCAAAGCCCACAAGTCAGTGGCATCAT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
37371 TTCAAAGCCCATAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
37399 TTCAAAGCCCACAAGTCAGTAGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
37427 TTCAAAGCCCACGAGTC
1 TTCAAAGCCCACAAGTC
37444 GATGGCGACA
Statistics
Matches: 310, Mismatches: 44, Indels: 30
0.81 0.11 0.08
Matches are distributed among these distances:
28 150 0.48
29 56 0.18
30 40 0.13
31 8 0.03
32 50 0.16
33 4 0.01
34 2 0.01
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.22
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:37142 original size:32 final size:32
Alignment explanation
Indices: 37099--37381 Score: 219
Period size: 32 Copynumber: 9.5 Consensus size: 32
37089 GTCAATCGCA
*
37099 TCATTTCAAAGCCCACTCAAGTCGGTGGCAAC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* *
37131 TCATTTGAAAGCCCACACAAGTCAGTGGC-A-
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
** *
37161 TCATTTCAAAGCCTGCACAAGTCGGTGACAAC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* *
37193 TCATTTCAAAGCCCACACAAGTTGATGGCAAC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* * * **
37225 CCATTTCATAG-CC-CATAAGTTAGTGGC-AC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* **
37254 -CCTTTCAAAGCCCACA-AA-TTAGTGGC-AC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* * *
37282 TCTTTTCAAA-ACC-CACAAGTCAGTGGC-AC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* *
37311 -CCTTTCAAAG-CC-CACAAGTCAGTGGC-AC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* *
37339 TCTTTTCAAAG-CC-CACAAGTCAGTGGC-A-
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
37367 TCATTTCAAAGCCCA
1 TCATTTCAAAGCCCA
37382 TAAGTTAGTG
Statistics
Matches: 214, Mismatches: 26, Indels: 24
0.81 0.10 0.09
Matches are distributed among these distances:
27 2 0.01
28 58 0.27
29 51 0.24
30 37 0.17
31 4 0.02
32 62 0.29
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.23
Consensus pattern (32 bp):
TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
Found at i:37311 original size:57 final size:57
Alignment explanation
Indices: 37047--37438 Score: 387
Period size: 57 Copynumber: 6.7 Consensus size: 57
37037 CGTTCATCTC
* * * *
37047 TTCAAAGTCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAATCGCA-TCAT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAATCAGTGGCACTCAT
* * *
37103 TTCAAAGCCCACTCAAGTCGGTGGCAACTCATTTGAAAGCCCACACAAGTCAGTGGCA-TCAT
1 TTCAAAGCCCA--CAAGTCAGTGGC-AC-CCTTTCAAAGCCCACA-AA-TCAGTGGCACTCAT
* * * * *
37165 TTCAAAGCCTGCACAAGTCGGTGACAACTCATTTCAAAGCCCACACAAGT-TGATGGCAACCCAT
1 TTCAAAGCC--CACAAGTCAGTGGC-AC-CCTTTCAAAGCCCACA-AA-TCAG-TGGC-ACTCAT
* * * * *
37229 TTCATAGCCCATAAGTTAGTGGCACCCTTTCAAAGCCCACAAATTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAATCAGTGGCACTCAT
* * *
37286 TTCAAAACCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAATCAGTGGCACTCAT
* * * * * *
37343 TTCAAAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCATAAGTTAGTGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAATCAGTGGCACTCAT
*
37399 TTCAAAGCCCACAAGTCAGTAGCACCCTTTCAAAGCCCAC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCAC
37439 GAGTCGATGG
Statistics
Matches: 288, Mismatches: 36, Indels: 24
0.83 0.10 0.07
Matches are distributed among these distances:
56 48 0.17
57 103 0.36
58 16 0.06
59 5 0.02
60 29 0.10
61 4 0.01
62 69 0.24
63 1 0.00
64 13 0.05
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (57 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAATCAGTGGCACTCAT
Found at i:37335 original size:85 final size:85
Alignment explanation
Indices: 37047--37443 Score: 431
Period size: 85 Copynumber: 4.5 Consensus size: 85
37037 CGTTCATCTC
* * *
37047 TTCAAAGTCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAATCGCATCATTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCATTTCAAAGCC
* *
37112 CACTCAAGTCGGTGGCAACTCAT
66 CA--CAAGTCAGTGGCAAC-CCT
* * * * *
37135 TTGAAAGCCCACACAAGTCAGTGGCATCATTTCAAAGCCTGCACAAGTCGGTGACAACTCATTTC
1 TTCAAAG-CC-CACAAGTCAGTGGCACCCTTTCAAAGCC--CACAAGTCAGTGGC-A-TCATTTC
*
37200 AAAGCCCACACAAGT-TGATGGCAACCCAT
60 AAAG-CC-CACAAGTCAG-TGGCAACCC-T
* * * * * * *
37229 TTCATAGCCCATAAGTTAGTGGCACCCTTTCAAAGCCCACAAATTAGTGGCACTCTTTTCAAAAC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA-TCATTTCAAAGC
37294 CCACAAGTCAGTGGC-ACCCT
65 CCACAAGTCAGTGGCAACCCT
*
37314 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCATTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCATCATTTCAAAGC
* *
37379 CCATAAGTTAGTGGC-ACCCT
65 CCACAAGTCAGTGGCAACCCT
* *
37399 TTCAAAGCCCACAAGTCAGTAGCACCCTTTCAAAGCCCACGAGTC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTC
37444 GATGGCGACA
Statistics
Matches: 261, Mismatches: 36, Indels: 28
0.80 0.11 0.09
Matches are distributed among these distances:
84 18 0.07
85 75 0.29
86 28 0.11
87 11 0.04
88 9 0.03
89 12 0.05
90 36 0.14
92 34 0.13
93 5 0.02
94 29 0.11
95 2 0.01
96 2 0.01
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.22
Consensus pattern (85 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCATTTCAAAGCC
CACAAGTCAGTGGCAACCCT
Found at i:37614 original size:45 final size:48
Alignment explanation
Indices: 37550--37669 Score: 147
Period size: 49 Copynumber: 2.5 Consensus size: 48
37540 CTGTCTGACA
* * *
37550 TCGCTAGCATTGAATCAGCATATTGG-CAC-CTTT-ATTAGCCCAATG
1 TCGCTGGCCTTGAATCAGCACATTGGCCACTCTTTCATTAGCCCAATG
* *
37595 TCGCTGGCCTTGAATCAGCACATTGGTCCACTTTTTCTTTAGCCCAATG
1 TCGCTGGCCTTGAATCAGCACATTGG-CCACTCTTTCATTAGCCCAATG
**
37644 TCGCTGGCCTTGAATTGGCACATTGG
1 TCGCTGGCCTTGAATCAGCACATTGG
37670 TACTCCTCTC
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
45 23 0.36
47 3 0.05
48 3 0.05
49 35 0.55
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.33
Consensus pattern (48 bp):
TCGCTGGCCTTGAATCAGCACATTGGCCACTCTTTCATTAGCCCAATG
Found at i:42816 original size:13 final size:15
Alignment explanation
Indices: 42798--42830 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
42788 TTTTTATTTT
42798 AAAAATG-AA-AATA
1 AAAAATGTAATAATA
42811 AAAAATGTAATAATA
1 AAAAATGTAATAATA
42826 AAAAA
1 AAAAA
42831 AGATTAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 2 0.11
15 9 0.50
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (15 bp):
AAAAATGTAATAATA
Done.