Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1466
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: 620546
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.34
File 3 of 3
Found at i:619556 original size:162 final size:155
Alignment explanation
Indices: 619148--619805 Score: 642
Period size: 162 Copynumber: 4.1 Consensus size: 155
619138 ATCTTTAAGT
* * * *
619148 CCACAACTCCGTGGCACCCTTT-TAAAAGCCCACAATTCCGTGGCACTTTTTTCATCTTT--AAG
1 CCACAACT-CGTGGCACTCTTTGT-AAAGCCCACAACTCCGTGGCACCTTTTTC-T-TTTCAAAA
* * * * * * *
619210 TCCACAAACTCCGTGGCACCCTTTTAAAGCCCACAATTCTGTGGCACTTTTTTCATCTTT-AAGT
62 CCCAC-AACTCCGTGGCACTC-TTTAAAGCCCACAACTCCGTGGCACCTTCTTC-TTTTTAAAG-
* *
619274 CCACAACTCCGTGGCACC--C--GTTT--AAGC
123 CCACAGCTCCGTGGCACCTTCTTCTTTCAAAGC
* * * * *
619301 CAAAAACTACGTGGCACCTTTTTTTTTTTATAAGCCCAC-ACTCCGTGGCACCTTTTTCTGTT-A
1 CCACAACT-CGTGGCA-C----TCTTTGTA-AAGCCCACAACTCCGTGGCACCTTTTTCTTTTCA
*
619364 AAGCCCACAACTCCGTGGCACTCTTTAAAGCCCACAACTCCGTGGGCACCTTCTTCTTTTTAAAG
59 AAACCCACAACTCCGTGGCACTCTTTAAAGCCCACAACTCCGT-GGCACCTTCTTCTTTTTAAAG
619429 CCACAGCTCCGTGGCACCTTCTTCTTTTCAAAGC
123 CCACAGCTCCGTGGCACCTTCTTC-TTTCAAAGC
* * *
619463 CCACGACTACGGGGCAACTCTTTGTAAAGCCCACAACTCAGTGGCACTCTTTTTCTCTTTTCAAA
1 CCACAACT-CGTGGC-ACTCTTTGTAAAGCCCACAACTCCGTGGCAC-C-TTTT-TCTTTTCAAA
*
619528 ACCCACGACTCCGTGGCACTCTTTAAAGCCCACAACTCCGTGGCAACCTTCTTCTTTTTAAAGCC
61 ACCCACAACTCCGTGGCACTCTTTAAAGCCCACAACTCCGTGGC-ACCTTCTTCTTTTTAAAG-C
619593 CACAGCTCCGTGGCACCTTCTTCGTTTC-AAGC
124 CACAGCTCCGTGGCACCTTCTTC-TTTCAAAGC
* *
619625 CCACAACTCGTGGCACTCTTTTTAAAGCCCACAACTCCGTGGCACCTTCTTC-TTTCAAAAGCCC
1 CCACAACTCGTGGCACTCTTTGTAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTCAAAA-CCC
* * * * *
619689 ACAACGCCGTGGCACCCTTTTAAAGCCCACAATTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCA
65 ACAACTCCGTGGCACTC-TTTAAAGCCCACAACTCCGTGGCAC-CTTCTT--CTTTTTAAAGCCA
* * *
619754 CAACTCCGTGGCACTTTTTTCTTTCAAAGC
126 CAGCTCCGTGGCACCTTCTTCTTTCAAAGC
619784 CCACAACTCCGTGGCACTCTTT
1 CCACAACT-CGTGGCACTCTTT
619806 TTCCCTTTTA
Statistics
Matches: 431, Mismatches: 42, Indels: 57
0.81 0.08 0.11
Matches are distributed among these distances:
153 13 0.03
154 1 0.00
155 39 0.09
156 37 0.09
157 38 0.09
158 72 0.17
159 44 0.10
160 58 0.13
161 13 0.03
162 87 0.20
163 29 0.07
ACGTcount: A:0.22, C:0.34, G:0.14, T:0.29
Consensus pattern (155 bp):
CCACAACTCGTGGCACTCTTTGTAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTCAAAACCCA
CAACTCCGTGGCACTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTTAAAGCCACAGCT
CCGTGGCACCTTCTTCTTTCAAAGC
Found at i:619755 original size:36 final size:36
Alignment explanation
Indices: 619703--619844 Score: 213
Period size: 36 Copynumber: 4.1 Consensus size: 36
619693 CGCCGTGGCA
*
619703 CCCTTTTAAAGCCCACAATTCCGTGGCACTCTTTTT
1 CCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
619739 CCCTTTTCAAAG-CCACAACTCCGTGGCACT-TTTTT
1 CCCTTTT-AAAGCCCACAACTCCGTGGCACTCTTTTT
*
619774 --CTTTCAAAGCCCACAACTCCGTGGCACTCTTTTT
1 CCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
*
619808 CCCTTTTAAAGTCCACAACTCCGTGGCA-TCTTTTT
1 CCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
619843 CC
1 CC
619845 TTCCCAAGCC
Statistics
Matches: 97, Mismatches: 4, Indels: 11
0.87 0.04 0.10
Matches are distributed among these distances:
32 4 0.04
33 22 0.23
34 5 0.05
35 14 0.14
36 48 0.49
37 4 0.04
ACGTcount: A:0.20, C:0.35, G:0.11, T:0.35
Consensus pattern (36 bp):
CCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
Found at i:619795 original size:69 final size:66
Alignment explanation
Indices: 619332--619858 Score: 414
Period size: 62 Copynumber: 8.1 Consensus size: 66
619322 TTTTTTTTAT
* *
619332 AAGCCCAC-ACTCCGTGGCACCTTTTTCTGTT-AAAGCCCACAACTCCGTGGCA---C-TCTTT-
1 AAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACTTCTTCTTTC
619390 A
66 A
* *
619391 AAGCCCACAACTCCGTGGGCACCTTCTTCTTTTTAAAG-CCACAGCTCCGTGGCACCTTCTTCTT
1 AAGCCCACAACTCCGT-GGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCA-CTTCTTC-T
619455 TTCA
63 TTCA
* * * * * * *
619459 AAGCCCACGACTACGGGGCAAC-TC-T-TTGT-AAAGCCCACAACTCAGTGGCACTCTTTTTCTC
1 AAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCA--C-TTCT-TC
619520 TTTTCA
62 -TTTCA
* *
619526 AAACCCACGACTCCGTGGCA----C-TC-TTT-AAAGCCCACAACTCCGTGGCAACCTTCTTCTT
1 AAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGC-A-CTTCTTC-T
*
619584 TTTA
63 TTCA
* *
619588 AAGCCCACAGCTCCGTGGCACCTTCTTCGTTTC-AAGCCCACAACT-CGTGGCAC-TCTT-TTT-
1 AAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACTTCTTCTTTC
619648 A
66 A
*
619649 AAGCCCACAACTCCGTGGCACCTTCTTC-TTTCAAAAGCCCACAACGCCGTGGCAC--C--CTTT
1 AAGCCCACAACTCCGTGGCACCTTCTTCTTTTC-AAAGCCCACAACTCCGTGGCACTTCTTCTTT
*
619709 TA
65 CA
* * *
619711 AAGCCCACAATTCCGTGGCACTCTTTTTCCCTTTTCAAAG-CCACAACTCCGTGGCACTTTTTTC
1 AAGCCCACAACTCCGTGGCAC-CTTCTT--CTTTTCAAAGCCCACAACTCCGTGGCAC-TTCTTC
619775 TTTCA
62 TTTCA
* * *
619780 AAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT-AAAGTCCACAACTCCGTGGCATCTTTTTC
1 AAGCCCACAACTCCGTGGCAC-CTTCTT--CTTTTCAAAGCCCACAACTCCGTGGCA-CTTCTT-
* *
619844 CTTCCC
61 CTTTCA
619850 AAGCCCACA
1 AAGCCCACA
619859 CAAGTCGGTG
Statistics
Matches: 395, Mismatches: 33, Indels: 69
0.79 0.07 0.14
Matches are distributed among these distances:
59 8 0.02
60 11 0.03
61 60 0.15
62 64 0.16
63 20 0.05
64 61 0.15
65 10 0.03
66 13 0.03
67 41 0.10
68 33 0.08
69 60 0.15
70 14 0.04
ACGTcount: A:0.22, C:0.35, G:0.14, T:0.29
Consensus pattern (66 bp):
AAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACTTCTTCTTTC
A
Found at i:619891 original size:32 final size:32
Alignment explanation
Indices: 619844--619934 Score: 118
Period size: 32 Copynumber: 2.9 Consensus size: 32
619834 CATCTTTTTC
*
619844 CTTCCCAAGCCCACACAAGTCGGTGGCAAC-G
1 CTTCCAAAGCCCACACAAGTCGGTGGCAACTG
* *
619875 CTTCCTAAAGCCCACACAAGTCGGTGGCACCTT
1 CTTCC-AAAGCCCACACAAGTCGGTGGCAACTG
619908 CTTCCAAAG-CCACACAAG-C-GTGGCAAC
1 CTTCCAAAGCCCACACAAGTCGGTGGCAAC
619935 CCCTCTAACC
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
29 7 0.13
30 1 0.02
31 14 0.26
32 27 0.50
33 5 0.09
ACGTcount: A:0.27, C:0.37, G:0.20, T:0.15
Consensus pattern (32 bp):
CTTCCAAAGCCCACACAAGTCGGTGGCAACTG
Found at i:620134 original size:49 final size:49
Alignment explanation
Indices: 619944--620452 Score: 523
Period size: 47 Copynumber: 10.5 Consensus size: 49
619934 CCCCTCTAAC
*
619944 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCCTTTTCCATCTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCA---TCTT-CATCTTTAAGT
* * * * *
619997 CTAATGTAGCTGGCCTTGACTCAGGCACATTGGCACCTTCATCTTTAAGT
1 CCAATATAGCTGGCCTTGAATCA-GCATATTGGCATCTTCATCTTTAAGT
*
620047 CCAATATCGCTGGCC-TGAATCAGCATATTGGCATCTTCATCTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGT
*
620095 CCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTT-AGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGT
* * * * *
620143 CCAATGT-GCTGGCCTTGACTCAGCACATTGGCA-CCTCATCGTT-AGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGT
*
620189 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCA--TCTT-CATCTTTAAGT
* * * * *
620241 CCAATGTAGCTGGCCTTTACTCAGCACATT-GC-CCTTCATCTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGT
* * *
620288 CCAATATCGCTGGCCTTGAATCAGC-T-GTGGCCCTCTTCATCTTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGG-CATCTTCATC-TTTAAGT
* * * *
620337 CCAATGTAGCTGGCC-TGACTTCA-CACATTGGCA----C--CTTTAAGA
1 CCAATATAGCTGGCCTTGA-ATCAGCATATTGGCATCTTCATCTTTAAGT
* *
620379 GC-ATATCGCTGGCCTTGAATCAGCATATTGGCTATCTTCATCTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGC-ATCTTCATCTTTAAGT
*
620428 CCAATGTAGCTGGCCTTGAATCAGC
1 CCAATATAGCTGGCCTTGAATCAGC
620453 CACCATTGGC
Statistics
Matches: 379, Mismatches: 52, Indels: 53
0.78 0.11 0.11
Matches are distributed among these distances:
41 13 0.03
42 18 0.05
43 2 0.01
45 2 0.01
46 18 0.05
47 82 0.22
48 61 0.16
49 67 0.18
50 47 0.12
51 10 0.03
52 29 0.08
53 20 0.05
54 10 0.03
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.33
Consensus pattern (49 bp):
CCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGT
Found at i:620253 original size:146 final size:148
Alignment explanation
Indices: 619944--620509 Score: 576
Period size: 146 Copynumber: 3.9 Consensus size: 148
619934 CCCCTCTAAC
* *
619944 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCCTTTTCCATCTTTAAGTCTAATGTAGCTG
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCA---TCTT-CATCTTTAAGTCCAATGTAGCTG
* *
620009 GCCTTGACTCAGGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTGAATCAGCATA
62 GCCTTGAATCA-GCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTGAATCAGCATA
*
620074 TTGGCA--TCTTCATCTTTAAGT
126 TTGGCACCTTTTCATCTTTAAGT
*
620095 CCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTT-AGTCCAATGT-GCTGGCCT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCT
* *
620158 TGACTCAGCACATTGGCACC-TCATCGTT-AGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
66 TGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCC-TGAATCAGCATATTGG
620221 CACCTTTTCCATCTTTAAGT
130 CACCTTTT-CATCTTTAAGT
* * * * * * *
620241 CCAATGTAGCTGGCCTTTACTCAGCACATT-GC-CCTTCATCTTTAAGTCCAATATCGCTGGCCT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCT
* * * *
620304 TGAATCAG--C-TGTGGCCCTCTTCATCTTTTAAGTCCAATGTAGCTGGCCTGACTTCA-CACAT
66 TGAATCAGCACAT-TGGCAC-CTTCATC-TTTAAGTCCAATATAGCTGGCCTGA-ATCAGCATAT
620365 TGGCACC-TTT-A-----AGAG-
127 TGGCACCTTTTCATCTTTA-AGT
*
620380 -C-ATATCGCTGGCCTTGAATCAGCATATTGGCTATCTTCATCTTTAAGTCCAATGTAGCTGGCC
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGC-ATCTTCATCTTTAAGTCCAATGTAGCTGGCC
* * *
620443 TTGAATCAGCCACCATTGGCA-C--CA--TTTAAGGTCCAA-GTAGCCTGGCTTGCATCAGCATA
65 TTGAATCAG-CA-CATTGGCACCTTCATCTTTAA-GTCCAATATAG-CTGGCCTGAATCAGCATA
620502 TTGGCACC
126 TTGGCACC
620510 ACGTTTCATC
Statistics
Matches: 359, Mismatches: 32, Indels: 61
0.79 0.07 0.13
Matches are distributed among these distances:
137 34 0.09
138 27 0.08
139 1 0.00
140 40 0.11
142 18 0.05
143 26 0.07
144 35 0.10
145 31 0.09
146 68 0.19
147 23 0.06
148 23 0.06
151 33 0.09
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (148 bp):
CCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCT
TGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTGAATCAGCATATTGGC
ACCTTTTCATCTTTAAGT
Found at i:620465 original size:241 final size:243
Alignment explanation
Indices: 619944--620452 Score: 691
Period size: 241 Copynumber: 2.1 Consensus size: 243
619934 CCCCTCTAAC
*
619944 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCCTTTTCCATCTTTAAGTCTAATGTAGCTG
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CCTTTTCCATCTTTAAGTCCAATGTAGCTG
620009 GCCTTGACTCAGGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTGAATCAGCATA
65 GCCTTGACTCAGGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTGAATCAGCATA
* * *
620074 TTGGCATCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
130 GTGGCATCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATC-TCATCTT
* * * *
620139 TAGTCCAATGTGCTGGCCTTGACTCAGCACATTGGCACCTCATCGTTAGT
194 AAGACCAATGCGCTGGCCTTGAATCAGCACATTGGCACCTCATCGTTAGT
620189 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGG
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGG
*
620254 CCTTTACTCA-GCACATT-GC-CCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGC-T-
66 CCTTGACTCAGGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCC-TGAATCAGCATA
* * *
620314 GTGGCCCTCTTCATCTTTTAAGTCCAATGTAGCTGGCC-TGACTTCA-CACATTGGCA-C-C-T-
130 GTGG-CATCTTCATC-TTTAAGTCCAATATAGCTGGCCTTGA-ATCAGCACATTGGCATCTCATC
* * * *
620373 TTAAGAGCATAT-CGCTGGCCTTGAATCAGCATATTGGCTATCTTCATCTTTAAGT
192 TTAAGACCA-ATGCGCTGGCCTTGAATCAGCACATTGGC-A-CCTCATCGTT-AGT
*
620428 CCAATGTAGCTGGCCTTGAATCAGC
1 CCAATATAGCTGGCCTTGAATCAGC
620453 CACCATTGGC
Statistics
Matches: 239, Mismatches: 17, Indels: 22
0.86 0.06 0.08
Matches are distributed among these distances:
236 29 0.12
237 4 0.02
238 9 0.04
239 27 0.11
240 4 0.02
241 52 0.22
242 34 0.14
243 7 0.03
244 39 0.16
245 34 0.14
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.33
Consensus pattern (243 bp):
CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGG
CCTTGACTCAGGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTGAATCAGCATAG
TGGCATCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTCATCTTAA
GACCAATGCGCTGGCCTTGAATCAGCACATTGGCACCTCATCGTTAGT
Found at i:620497 original size:46 final size:44
Alignment explanation
Indices: 620330--620510 Score: 149
Period size: 50 Copynumber: 4.0 Consensus size: 44
620320 CTCTTCATCT
*
620330 TTTAAGTCCAATGTAGCTGGCC-TGACTTCA-CACATTGGCACC-
1 TTTAAGTCCAATGTAGCTGGCCTTGA-ATCAGCACATTGGCACCA
** * * *
620372 TTTAAGAGC-ATATCGCTGGCCTTGAATCAGCATATTGGCTATCTTCA
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGC-A-C--CA
620419 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCCACCATTGGCACCA
1 --TTTAAGTCCAATGTAGCTGGCCTTGAATCAG-CA-CATTGGCACCA
* *
620467 TTTAAGGTCCAA-GTAGCCTGG-CTTGCATCAGCATATTGGCACCA
1 TTTAA-GTCCAATGTAG-CTGGCCTTGAATCAGCACATTGGCACCA
620511 CGTTTCATCT
Statistics
Matches: 112, Mismatches: 13, Indels: 26
0.74 0.09 0.17
Matches are distributed among these distances:
41 13 0.12
42 18 0.16
43 1 0.01
44 11 0.10
45 2 0.02
46 19 0.17
47 10 0.09
48 2 0.02
49 7 0.06
50 20 0.18
51 3 0.03
52 6 0.05
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (44 bp):
TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCA
Done.