Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2327
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: 26122
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:294 original size:64 final size:63
Alignment explanation
Indices: 210--424 Score: 262
Period size: 64 Copynumber: 3.4 Consensus size: 63
200 AATGGCAATC
* * *
210 TCTTCTCAAAGCCCACGACTCAGTGGCATTTTGTCCTAAAGTCCACGACTCCGTGGCACCTTTT
1 TCTT-TCAAAGTCCACGACTCAGTGGCATTTTGTCCTAAAGTCCATGACTCAGTGGCACCTTTT
*
274 TCTTCTCAAAG-CCTACGACTCAGTGGCATTTTGTCCTAAAGTCCATGACTCAGTGGCATCC-TC
1 TCTT-TCAAAGTCC-ACGACTCAGTGGCATTTTGTCCTAAAGTCCATGACTCAGTGGCA-CCTTT
337 T
63 T
* * * *
338 T-TTTCAAAGTCCATGACTCAATGGCATTTAGT-CTCAAAGTCCATGACTCAGTGGCA-TTTTT
1 TCTTTCAAAGTCCACGACTCAGTGGCATTTTGTCCT-AAAGTCCATGACTCAGTGGCACCTTTT
*
399 TC-TTCAAAGTCCACGACTCCGTGGCA
1 TCTTTCAAAGTCCACGACTCAGTGGCA
425 CCCTTTTAAG
Statistics
Matches: 134, Mismatches: 11, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
61 26 0.19
62 44 0.33
63 6 0.04
64 56 0.42
65 2 0.01
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.31
Consensus pattern (63 bp):
TCTTTCAAAGTCCACGACTCAGTGGCATTTTGTCCTAAAGTCCATGACTCAGTGGCACCTTTT
Found at i:423 original size:31 final size:31
Alignment explanation
Indices: 180--424 Score: 216
Period size: 30 Copynumber: 7.9 Consensus size: 31
170 CTTCAAATAC
* *
180 TTTCTT-AAAGTCCACGACTCAATGGCAATCT
1 TTTCTTCAAAGTCCACGACTCAGTGGC-ATTT
* *
211 CTTC-TCAAAGCCCACGACTCAGTGGCATTT
1 TTTCTTCAAAGTCCACGACTCAGTGGCATTT
* * * *
241 TGTCCT-AAAGTCCACGACTCCGTGGCACCTT
1 TTTCTTCAAAGTCCACGACTCAGTGGCA-TTT
272 TTTCTTCTCAAAG-CCTACGACTCAGTGGCATTT
1 TTTC-T-TCAAAGTCC-ACGACTCAGTGGCATTT
* * * *
305 TGTCCT-AAAGTCCATGACTCAGTGGCATCCTC
1 TTTCTTCAAAGTCCACGACTCAGTGGCAT--TT
* *
337 TTT-TTCAAAGTCCATGACTCAATGGCATTT
1 TTTCTTCAAAGTCCACGACTCAGTGGCATTT
** *
367 AGTC-TCAAAGTCCATGACTCAGTGGCATTT
1 TTTCTTCAAAGTCCACGACTCAGTGGCATTT
*
397 TTTCTTCAAAGTCCACGACTCCGTGGCA
1 TTTCTTCAAAGTCCACGACTCAGTGGCA
425 CCCTTTTAAG
Statistics
Matches: 173, Mismatches: 28, Indels: 26
0.76 0.12 0.11
Matches are distributed among these distances:
30 72 0.42
31 52 0.30
32 24 0.14
33 8 0.05
34 17 0.10
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.31
Consensus pattern (31 bp):
TTTCTTCAAAGTCCACGACTCAGTGGCATTT
Found at i:472 original size:34 final size:33
Alignment explanation
Indices: 426--690 Score: 235
Period size: 34 Copynumber: 8.0 Consensus size: 33
416 TCCGTGGCAC
426 CCTTT-TAAGCCCACAACTCCGTGGCACCTTTT
1 CCTTTCTAAGCCCACAACTCCGTGGCACCTTTT
* * *
458 CCTTTTTGGAGCCCAGAACTCCGTGGCACCTTTT
1 CCTTTCT-AAGCCCACAACTCCGTGGCACCTTTT
*
492 TCTTTCTAAAGCCCACAACTCCGTGGCACTCTTTTT
1 CCTTTCT-AAGCCCACAACTCCGTGGCAC-C-TTTT
*
528 CC-TTCTAAGTCCACAACTCCGTGGCA-C----
1 CCTTTCTAAGCCCACAACTCCGTGGCACCTTTT
* * * *
555 CCGTT-TGAGCCCACAACTCTGTGGCATCTTTTT
1 CCTTTCTAAGCCCACAACTCCGTGGCA-CCTTTT
* *
588 CCTTTTTAAAGCCTACAACTCCGTGGCACTCTTTTT
1 CCTTTCT-AAGCCCACAACTCCGTGGCAC-C-TTTT
*
624 CC-TTCTAAGTCCACAACTCCGTGGCACTCTTTCT
1 CCTTTCTAAGCCCACAACTCCGTGGCAC-CTTT-T
* *
658 CC-TTCTAAGTCCACAACTCTGTGGCACCCTTTT
1 CCTTTCTAAGCCCACAACTCCGTGGCA-CCTTTT
691 ACGTCCACAG
Statistics
Matches: 194, Mismatches: 22, Indels: 33
0.78 0.09 0.13
Matches are distributed among these distances:
27 20 0.10
28 2 0.01
32 6 0.03
33 9 0.05
34 120 0.62
35 26 0.13
36 11 0.06
ACGTcount: A:0.18, C:0.35, G:0.14, T:0.33
Consensus pattern (33 bp):
CCTTTCTAAGCCCACAACTCCGTGGCACCTTTT
Found at i:621 original size:96 final size:95
Alignment explanation
Indices: 466--650 Score: 316
Period size: 96 Copynumber: 1.9 Consensus size: 95
456 TTCCTTTTTG
*
466 GAGCCCAGAACTCCGTGGCACCTTTTTCTTTCTAAAGCCCACAACTCCGTGGCACTCTTTTTCCT
1 GAGCCCACAACTCCGTGGCACCTTTTTCTTTCTAAAGCCCACAACTCCGTGGCACTCTTTTTCCT
531 TCTAAGTCCACAACTCCGTGGCACCCGTTT
66 TCTAAGTCCACAACTCCGTGGCACCCGTTT
* * * *
561 GAGCCCACAACTCTGTGGCATCTTTTTCCTTTTTAAAGCCTACAACTCCGTGGCACTCTTTTTCC
1 GAGCCCACAACTCCGTGGCACCTTTTT-CTTTCTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
626 TTCTAAGTCCACAACTCCGTGGCAC
65 TTCTAAGTCCACAACTCCGTGGCAC
651 TCTTTCTCCT
Statistics
Matches: 84, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
95 24 0.29
96 60 0.71
ACGTcount: A:0.19, C:0.35, G:0.15, T:0.31
Consensus pattern (95 bp):
GAGCCCACAACTCCGTGGCACCTTTTTCTTTCTAAAGCCCACAACTCCGTGGCACTCTTTTTCCT
TCTAAGTCCACAACTCCGTGGCACCCGTTT
Found at i:661 original size:130 final size:129
Alignment explanation
Indices: 400--735 Score: 451
Period size: 130 Copynumber: 2.6 Consensus size: 129
390 GGCATTTTTT
* * *
400 CTTCAAAGTCCACGACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCA-CCTTTTCCTTTT
1 CTTCTAAGTCCACAACTCCGTGGCACCC-TTTAAGCCCACAACTCCGTGGCATCTTTTTCCTTTT
** * * *
464 TGGAGCCCAGAACTCCGTGGCACCTTTTTCTTTCTAAAGCCCACAACTCCGTGGCACTCTTTTTC
65 TAAAGCCCACAACTCCGTGGCACCTTTTTCCTTCTAAAGCCCACAACTCCGTGGCACTCTTTCTC
* *
529 CTTCTAAGTCCACAACTCCGTGGCACCCGTTTGAGCCCACAACTCTGTGGCATCTTTTTCCTTTT
1 CTTCTAAGTCCACAACTCCGTGGCACCC-TTTAAGCCCACAACTCCGTGGCATCTTTTTCCTTTT
* *
594 TAAAGCCTACAACTCCGTGGCACTCTTTTTCCTTCT-AAGTCCACAACTCCGTGGCACTCTTTCT
65 TAAAGCCCACAACTCCGTGGCAC-CTTTTTCCTTCTAAAGCCCACAACTCCGTGGCACTCTTTCT
658 C
129 C
* * * * * *
659 CTTCTAAGTCCACAACTCTGTGGCACCCTTTTACGTCCACAGCTCCGTGGCATCTTTCTCATTTT
1 CTTCTAAGTCCACAACTCCGTGGCACCC-TTTAAGCCCACAACTCCGTGGCATCTTTTTCCTTTT
724 TCAAAGCCCACA
65 T-AAAGCCCACA
736 CAAGTTGGTG
Statistics
Matches: 181, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
129 47 0.26
130 114 0.63
131 20 0.11
ACGTcount: A:0.19, C:0.35, G:0.14, T:0.32
Consensus pattern (129 bp):
CTTCTAAGTCCACAACTCCGTGGCACCCTTTAAGCCCACAACTCCGTGGCATCTTTTTCCTTTTT
AAAGCCCACAACTCCGTGGCACCTTTTTCCTTCTAAAGCCCACAACTCCGTGGCACTCTTTCTC
Found at i:691 original size:96 final size:90
Alignment explanation
Indices: 493--715 Score: 229
Period size: 96 Copynumber: 2.3 Consensus size: 90
483 GCACCTTTTT
*
493 CTTTCTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCG
1 CTTT-TAAAG-CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCC
*
558 TTTGAGCCCACAACTCTGTGGCATCTTTTTC
64 TTTAAGCCCACAACTCTGTGGCATC----TC
589 CTTTTTAAAGCCTACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACTCT
1 C-TTTTAAAGCC-ACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCA--C-
*
654 TTCTCCTTCTAAGTCCACAACTCTGTGGCA-C-C
61 --C-CCTT-TAAGCCCACAACTCTGTGGCATCTC
* *
686 CTTTT-ACGTCCACAGCTCCGTGGCA-TCTTT
1 CTTTTAAAG-CCACAACTCCGTGGCACTCTTT
716 CTCATTTTTC
Statistics
Matches: 112, Mismatches: 5, Indels: 22
0.81 0.04 0.16
Matches are distributed among these distances:
94 5 0.04
95 17 0.15
96 60 0.54
97 5 0.04
98 1 0.01
101 1 0.01
102 4 0.04
103 19 0.17
ACGTcount: A:0.18, C:0.35, G:0.14, T:0.33
Consensus pattern (90 bp):
CTTTTAAAGCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCCTT
TAAGCCCACAACTCTGTGGCATCTC
Found at i:756 original size:32 final size:32
Alignment explanation
Indices: 720--1008 Score: 323
Period size: 32 Copynumber: 8.9 Consensus size: 32
710 ATCTTTCTCA
720 TTTTTCAAAGCCCACACAAGTTGGTGGCAACC
1 TTTTTCAAAGCCCACACAAGTTGGTGGCAACC
*
752 TTTTTCCAAAGCCCACACAAGTCGGTGGCAACC
1 TTTTT-CAAAGCCCACACAAGTTGGTGGCAACC
* *
785 ATTCTCAAAGCCCACACAAGTTGGTGGCAACC
1 TTTTTCAAAGCCCACACAAGTTGGTGGCAACC
* *
817 TTTTTCTAAAGCCCACCACAAGTCGGTGACAACC
1 TTTTTC-AAAGCCCA-CACAAGTTGGTGGCAACC
* *
851 TTCTTCAAAGCCCACACAAGTTGGTGGCAACTT
1 TTTTTCAAAGCCCACACAAGTTGGTGGCAAC-C
* * *
884 TTTTTTAAAGCCCACAGAAGTCGGTGGCAATCC
1 TTTTTCAAAGCCCACACAAGTTGGTGGCAA-CC
** *
917 CCTCT-AAAGCCCACACAAGTTGGTGGCAATCC
1 TTTTTCAAAGCCCACACAAGTTGGTGGCAA-CC
** * *
949 CCTCT-AAAGCCCACACAAGTCGGTGGCAACC
1 TTTTTCAAAGCCCACACAAGTTGGTGGCAACC
* *
980 TTCTTCAAAACCC-CACACAGTTGGTGGCA
1 TTTTTCAAAGCCCACACA-AGTTGGTGGCA
1009 TCTTCCTTTA
Statistics
Matches: 221, Mismatches: 29, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
31 7 0.03
32 119 0.54
33 73 0.33
34 22 0.10
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.22
Consensus pattern (32 bp):
TTTTTCAAAGCCCACACAAGTTGGTGGCAACC
Found at i:793 original size:65 final size:65
Alignment explanation
Indices: 723--1008 Score: 395
Period size: 65 Copynumber: 4.4 Consensus size: 65
713 TTTCTCATTT
*
723 TTCAAAGCCCACACAAGTTGGTGGCAACCTTTTTCCAAAGCCCACACAAGTCGGTGGCAACCATT
1 TTCAAAGCCCACACAAGTTGGTGGCAACCTTTTTCTAAAGCCCACACAAGTCGGTGGCAACC-TT
788 C
65 C
*
789 -TCAAAGCCCACACAAGTTGGTGGCAACCTTTTTCTAAAGCCCACCACAAGTCGGTGACAACCTT
1 TTCAAAGCCCACACAAGTTGGTGGCAACCTTTTTCTAAAGCCCA-CACAAGTCGGTGGCAACCTT
853 C
65 C
* * *
854 TTCAAAGCCCACACAAGTTGGTGGCAACTTTTTTTTAAAGCCCACAGAAGTCGGTGGCAATCC--
1 TTCAAAGCCCACACAAGTTGGTGGCAACCTTTTTCTAAAGCCCACACAAGTCGGTGGCAA-CCTT
917 C
65 C
* **
918 CTCTAAAGCCCACACAAGTTGGTGGCAATCC--CCTCTAAAGCCCACACAAGTCGGTGGCAACCT
1 TTC-AAAGCCCACACAAGTTGGTGGCAA-CCTTTTTCTAAAGCCCACACAAGTCGGTGGCAACCT
981 TC
64 TC
*
983 TTCAAAACCC-CACACAGTTGGTGGCA
1 TTCAAAGCCCACACA-AGTTGGTGGCA
1009 TCTTCCTTTA
Statistics
Matches: 198, Mismatches: 14, Indels: 18
0.86 0.06 0.08
Matches are distributed among these distances:
63 6 0.03
64 45 0.23
65 86 0.43
66 61 0.31
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (65 bp):
TTCAAAGCCCACACAAGTTGGTGGCAACCTTTTTCTAAAGCCCACACAAGTCGGTGGCAACCTTC
Found at i:875 original size:131 final size:129
Alignment explanation
Indices: 723--1008 Score: 416
Period size: 131 Copynumber: 2.2 Consensus size: 129
713 TTTCTCATTT
*
723 TTCAAAGCCCACACAAGTTGGTGGCAACCTTTTTCCAAAGCCCACACAAGTCGGTGGCAA-CCAT
1 TTCAAAGCCCACACAAGTTGGTGGCAACCTTTTTCCAAAGCCCACACAAGTCGGTGGCAATCCAC
**
787 TCTCAAAGCCCACACAAGTTGGTGGCAA-CCTTTTTCTAAAGCCCACCACAAGTCGGTGACAACC
66 TCT-AAAGCCCACACAAGTTGGTGGCAATCC--CCTCTAAAGCCCA-CACAAGTCGGTGACAACC
851 TTC
127 TTC
* ** * *
854 TTCAAAGCCCACACAAGTTGGTGGCAACTTTTTTTTAAAGCCCACAGAAGTCGGTGGCAATCCCC
1 TTCAAAGCCCACACAAGTTGGTGGCAACCTTTTTCCAAAGCCCACACAAGTCGGTGGCAATCCAC
*
919 TCTAAAGCCCACACAAGTTGGTGGCAATCCCCTCTAAAGCCCACACAAGTCGGTGGCAACCTTC
66 TCTAAAGCCCACACAAGTTGGTGGCAATCCCCTCTAAAGCCCACACAAGTCGGTGACAACCTTC
*
983 TTCAAAACCC-CACACAGTTGGTGGCA
1 TTCAAAGCCCACACA-AGTTGGTGGCA
1009 TCTTCCTTTA
Statistics
Matches: 142, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
128 4 0.03
129 40 0.28
130 11 0.08
131 80 0.56
132 7 0.05
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (129 bp):
TTCAAAGCCCACACAAGTTGGTGGCAACCTTTTTCCAAAGCCCACACAAGTCGGTGGCAATCCAC
TCTAAAGCCCACACAAGTTGGTGGCAATCCCCTCTAAAGCCCACACAAGTCGGTGACAACCTTC
Found at i:1075 original size:43 final size:45
Alignment explanation
Indices: 1017--2047 Score: 823
Period size: 43 Copynumber: 21.9 Consensus size: 45
1007 CATCTTCCTT
* *
1017 TAAGTCCAGTATAGCTGGCCTTGAATCAGCACATTGGCACCTC-C
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTCTC
* * *
1061 -AAGTCCAATGTAGCTGGCCTTAAATCAGCACATTGGCACCT-T-
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTCTC
* *
1103 TAAGTCCAATATCGCTGGCCTTGAATCAG--TATTGGCACTTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCAC---C-TCTC
* *
1150 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CT-TC
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTCTC
* * *
1193 CAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC-TC-TC
* *
1240 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CT-TC
1 --TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTCTC
* * * *
1285 CAAGTCCAATATCGCTGGCCTTGAACCAGCATATTGACACCTTCATC
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC-TC-TC
* * *
1332 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCATC
1 --TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA--C-----CTC-TC
*
1387 TTTAAGTCCAATATCGCTGG-CTCTGAATCAGCATATTGGCACCTTCATC
1 --TAAGTCCAATATCGCTGGCCT-TGAATCAGCACATTGGCACC-TC-TC
* *
1436 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CT-TC
1 --TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTCTC
* *
1481 CAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC-TC-TC
* * *
1528 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACATCTTTTTTCTCATC
1 --TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA-C------CTC-TC
* *
1583 TTTAAGTCCAATATCGGTGG-CTCTGAATCAGCATATTGGCACCTTCATC
1 --TAAGTCCAATATCGCTGGCCT-TGAATCAGCACATTGGCACC-TC-TC
*
1632 TTTAAGTCCAAT-GCAGCTGGCCTTGAATCAGCACATTGGCACCTC-C
1 --TAAGTCCAATATC-GCTGGCCTTGAATCAGCACATTGGCACCTCTC
* *
1678 -AAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC-TC-TC
* *
1724 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTC-C
1 --TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTCTC
* *
1770 -AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGACACCTTCATC
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC-TC-TC
* * * *
1816 TTTAAGTCCAATGTAGCTGGCCTTGAATCAACACATTGGCAACTC-C
1 --TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTCTC
*
1862 -AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCCTCATC
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CCTC-TC
* * *
1908 TTTTAAG-CCTAATGTCGTTGGCCTTGAATCAGCACATTGGTACCT-T-
1 ---TAAGTCC-AATATCGCTGGCCTTGAATCAGCACATTGGCACCTCTC
* * *
1954 TAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATC
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC----TC-TC
* *
2004 TTTAAGTCCAATGTCGCCGGCCTTGAATCAGCACATTGGCACCT
1 --TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCT
2048 TCATCTTTAA
Statistics
Matches: 816, Mismatches: 91, Indels: 156
0.77 0.09 0.15
Matches are distributed among these distances:
41 8 0.01
43 305 0.37
44 15 0.02
45 9 0.01
46 7 0.01
47 37 0.05
48 12 0.01
49 265 0.32
50 36 0.04
51 1 0.00
52 36 0.04
53 1 0.00
54 5 0.01
55 77 0.09
56 2 0.00
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (45 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTCTC
Found at i:1268 original size:92 final size:92
Alignment explanation
Indices: 1018--2045 Score: 1409
Period size: 92 Copynumber: 11.0 Consensus size: 92
1008 ATCTTCCTTT
* * *
1018 AAGTCCAGTATAGCTGGCCTTGAATCAGCACATTGGCACC-TC--C---AAGTCCAATGTAGCTG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTG
* *
1077 GCCTTAAATCAGCACATTGGCACCTT-T
66 GCCTTGAATCAGCACATTGGCA-CTTCC
*
1104 AAGTCCAATATCGCTGGCCTTGAATCAG--TATTGGCACTTTCATCTTTAAGTCCAATGTAGCTG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTG
1167 GCCTTGAATCAGCACATTGGCACTTCC
66 GCCTTGAATCAGCACATTGGCACTTCC
*
1194 AAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTG
1259 GCCTTGAATCAGCACATTGGCACTTCC
66 GCCTTGAATCAGCACATTGGCACTTCC
* *
1286 AAGTCCAATATCGCTGGCCTTGAACCAGCATATTGACACCTTCATCTTTAAGTCCAATGTAGCTG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTG
*
1351 GCCTTGAATCAGCACATTGACATCCTTTTTCTCATC
66 GCCTTGAATCAGCACATTGGCA--C----T-TC--C
1387 TTTAAGTCCAATATCGCTGG-CTCTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
1 ---AAGTCCAATATCGCTGGCCT-TGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
1451 GCTGGCCTTGAATCAGCACATTGGCACTTCC
62 GCTGGCCTTGAATCAGCACATTGGCACTTCC
1482 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTG
*
1547 GCCTTGAATCAGCACATTGACATCTTTTTTCTCATC
66 GCCTTGAATCAGCACATTGGCA-C-----T-TC--C
* *
1583 TTTAAGTCCAATATCGGTGG-CTCTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGCA
1 ---AAGTCCAATATCGCTGGCCT-TGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
*
1647 GCTGGCCTTGAATCAGCACATTGGCACCTCC
62 GCTGGCCTTGAATCAGCACATTGGCACTTCC
*
1678 AAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTG
*
1743 GCCTTGAATCAGCACATTGGCACCTCC
66 GCCTTGAATCAGCACATTGGCACTTCC
*
1770 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGACACCTTCATCTTTAAGTCCAATGTAGCTG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTG
*
1835 GCCTTGAATCAACACATTGGCAAC-TCC
66 GCCTTGAATCAGCACATTGGC-ACTTCC
* * *
1862 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCCTCATCTTTTAAG-CCTAATGTCGT
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC-TTTAAGTCC-AATGTAGC
* *
1926 TGGCCTTGAATCAGCACATTGGTACCTT-T
64 TGGCCTTGAATCAGCACATTGGCA-CTTCC
* * *
1955 AAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCATCTTTAAGTCCAATGTAG
*
2020 CCGGCCTTGAATCAGCACATTGGCAC
63 CTGGCCTTGAATCAGCACATTGGCAC
2046 CTTCATCTTT
Statistics
Matches: 858, Mismatches: 38, Indels: 84
0.88 0.04 0.09
Matches are distributed among these distances:
84 8 0.01
85 2 0.00
86 26 0.03
87 1 0.00
89 3 0.00
90 64 0.07
92 447 0.52
93 79 0.09
94 3 0.00
95 37 0.04
96 7 0.01
97 4 0.00
98 3 0.00
99 4 0.00
101 2 0.00
102 1 0.00
103 5 0.01
104 162 0.19
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (92 bp):
AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTG
GCCTTGAATCAGCACATTGGCACTTCC
Found at i:1534 original size:196 final size:189
Alignment explanation
Indices: 1014--2045 Score: 1418
Period size: 196 Copynumber: 5.5 Consensus size: 189
1004 TGGCATCTTC
* * *
1014 CTTTAAGTCCAGTATAGCTGGCCTTGAATCAGCACATTGGCACC-TC--C---AAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
* *
1073 GCTGGCCTTAAATCAGCACATTGGCACCTT-TAAGTCCAATATCGCTGGCCTTGAATCAG--TAT
66 GCTGGCCTTGAATCAGCACATTGGCA-CTTCCAAGTCCAATATCGCTGGCCTTGAATCAGCATAT
* *
1135 TGGCACTTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CT--T
130 TGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACACCTCAT
* *
1192 C--CAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
*
1255 GCTGGCCTTGAATCAGCACATTGGCACTTCCAAGTCCAATATCGCTGGCCTTGAACCAGCATATT
66 GCTGGCCTTGAATCAGCACATTGGCACTTCCAAGTCCAATATCGCTGGCCTTGAATCAGCATATT
*
1320 GACACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCA
131 GGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACA--C-----CTCA
1385 T
189 T
1386 CTTTAAGTCCAATATCGCTGG-CTCTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
1 CTTTAAGTCCAATATCGCTGGCCT-TGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
1450 AGCTGGCCTTGAATCAGCACATTGGCACTTCCAAGTCCAATATCGCTGGCCTTGAATCAGCATAT
65 AGCTGGCCTTGAATCAGCACATTGGCACTTCCAAGTCCAATATCGCTGGCCTTGAATCAGCATAT
1515 TGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACATCTTTTTTCTC
130 TGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACA-C------CTC
1580 AT
188 AT
* *
1582 CTTTAAGTCCAATATCGGTGG-CTCTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGC
1 CTTTAAGTCCAATATCGCTGGCCT-TGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
* *
1646 AGCTGGCCTTGAATCAGCACATTGGCACCTCCAAGTCCAATATCGTTGGCCTTGAATCAGCATAT
65 AGCTGGCCTTGAATCAGCACATTGGCACTTCCAAGTCCAATATCGCTGGCCTTGAATCAGCATAT
*
1711 TGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTC--
130 TGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACACCTCAT
*
1769 C---AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGACACCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
*
1831 GCTGGCCTTGAATCAACACATTGGCAAC-TCCAAGTCCAATATCGCTGGCCTTGAATCAGCATAT
66 GCTGGCCTTGAATCAGCACATTGGC-ACTTCCAAGTCCAATATCGCTGGCCTTGAATCAGCATAT
* * * * *
1895 TGGCACCCTCATCTTTTAAG-CCTAATGTCGTTGGCCTTGAATCAGCACATTG----GT-AC
130 TGGCACCTTCATC-TTTAAGTCC-AATGTAGCTGGCCTTGAATCAGCACATTGACACCTCAT
* *
1951 CTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCATCTTTAAGTCCAAT
* *
2016 GTCGCCGGCCTTGAATCAGCACATTGGCAC
63 GTAGCTGGCCTTGAATCAGCACATTGGCAC
2046 CTTCATCTTT
Statistics
Matches: 783, Mismatches: 36, Indels: 61
0.89 0.04 0.07
Matches are distributed among these distances:
176 36 0.05
177 2 0.00
178 1 0.00
179 1 0.00
181 4 0.01
182 65 0.08
184 182 0.23
185 74 0.09
187 4 0.01
188 42 0.05
189 3 0.00
192 2 0.00
194 2 0.00
195 4 0.01
196 361 0.46
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.31
Consensus pattern (189 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
GCTGGCCTTGAATCAGCACATTGGCACTTCCAAGTCCAATATCGCTGGCCTTGAATCAGCATATT
GGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACACCTCAT
Found at i:2906 original size:13 final size:13
Alignment explanation
Indices: 2888--2912 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2878 CATAAAGTGT
2888 TGTATCAATACAA
1 TGTATCAATACAA
2901 TGTATCAATACA
1 TGTATCAATACA
2913 TAAGTTTTGT
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:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (13 bp):
TGTATCAATACAA
Found at i:2931 original size:32 final size:33
Alignment explanation
Indices: 2868--2933 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
2858 TTCAACGATT
*
2868 TGTATCGATACATAAAGTGTTGTATCAATACAA
1 TGTATCAATACATAAAGTGTTGTATCAATACAA
* *
2901 TGTATCAATACAT-AAGTTTTGTATCGATACAA
1 TGTATCAATACATAAAGTGTTGTATCAATACAA
2933 T
1 T
2934 ATAAGCTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 18 0.60
33 12 0.40
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (33 bp):
TGTATCAATACATAAAGTGTTGTATCAATACAA
Found at i:3132 original size:51 final size:51
Alignment explanation
Indices: 2987--3134 Score: 251
Period size: 52 Copynumber: 2.9 Consensus size: 51
2977 TTCGATACAT
***
2987 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-ATAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
3039 TGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAT-AAATGTATCGATACATGCAGGCAAATTTGCCCAGA
3091 TGTATCGATACACTATAAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACACTATAAATGTATCGATACATGCAGGCAAATTT
3135 TCATATTTTG
Statistics
Matches: 92, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
51 30 0.33
52 62 0.67
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Consensus pattern (51 bp):
TGTATCGATACACTATAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:9763 original size:18 final size:20
Alignment explanation
Indices: 9721--9773 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
9711 CTGCCAGTTT
9721 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTGAG
*
9741 TATGT-TCGATACAA-TGAG
1 CATGTATCGATACAATTGAG
9759 CATGTATCGATACAA
1 CATGTATCGATACAA
9774 CGTATCGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 8 0.27
19 18 0.60
20 4 0.13
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTGAG
Found at i:9780 original size:13 final size:13
Alignment explanation
Indices: 9762--9786 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9752 CAATGAGCAT
9762 GTATCGATACAAC
1 GTATCGATACAAC
9775 GTATCGATACAA
1 GTATCGATACAA
9787 AGCATAATAT
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:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (13 bp):
GTATCGATACAAC
Found at i:10431 original size:48 final size:48
Alignment explanation
Indices: 10378--10474 Score: 142
Period size: 48 Copynumber: 2.0 Consensus size: 48
10368 ATAAAACTCC
** *
10378 CCCTTAATAAAA-TTTTTCTCCCTTTTGATAACATAATAAAAATTTTCT
1 CCCTTAATAAAATTTTTTCTCCCCCTTGATAAAATAAT-AAAATTTTCT
*
10426 CCCTTAATAAAATTTTTTCTCCCCCTTGATAAAATAATAAATTTTTCT
1 CCCTTAATAAAATTTTTTCTCCCCCTTGATAAAATAATAAAATTTTCT
10474 C
1 C
10475 TCTCTTGATA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
48 22 0.50
49 22 0.50
ACGTcount: A:0.34, C:0.21, G:0.02, T:0.43
Consensus pattern (48 bp):
CCCTTAATAAAATTTTTTCTCCCCCTTGATAAAATAATAAAATTTTCT
Found at i:10452 original size:22 final size:20
Alignment explanation
Indices: 10411--10448 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
10401 TTTGATAACA
10411 TAATAAAA-ATTTTCTCCCT
1 TAATAAAATATTTTCTCCCT
*
10430 TAATAAAATTTTTTCTCCC
1 TAATAAAATATTTTCTCCC
10449 CCTTGATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (20 bp):
TAATAAAATATTTTCTCCCT
Found at i:10481 original size:28 final size:28
Alignment explanation
Indices: 10431--10495 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
10421 TTTCTCCCTT
*
10431 AATAA-AATTTTTTCTCCCCCTTGATAA
1 AATAATAAATTTTTCTCCCCCTTGATAA
* *
10458 AATAATAAATTTTTCTCTCTCTTGATAA
1 AATAATAAATTTTTCTCCCCCTTGATAA
*
10486 AGATATTAAA
1 A-ATAATAAA
10496 GCTCTCTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 5 0.16
28 20 0.62
29 7 0.22
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (28 bp):
AATAATAAATTTTTCTCCCCCTTGATAA
Found at i:12442 original size:20 final size:21
Alignment explanation
Indices: 12412--12451 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
12402 ATTTGGGTTT
12412 TTCAGATGTATCGATACATCA
1 TTCAGATGTATCGATACATCA
*
12433 TTCA-ATGTATTGATACATC
1 TTCAGATGTATCGATACATC
12452 CTGAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (21 bp):
TTCAGATGTATCGATACATCA
Found at i:16924 original size:12 final size:12
Alignment explanation
Indices: 16907--16937 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
16897 TGAGTCAACT
16907 TCATCATTATCA
1 TCATCATTATCA
*
16919 TCATCATTATCT
1 TCATCATTATCA
16931 TCATCAT
1 TCATCAT
16938 CTTTGATGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.45
Consensus pattern (12 bp):
TCATCATTATCA
Found at i:18557 original size:17 final size:17
Alignment explanation
Indices: 18535--18567 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
18525 GATACTTTTG
18535 ACAATGTATCGATACAT
1 ACAATGTATCGATACAT
18552 ACAATGTATCGATACA
1 ACAATGTATCGATACA
18568 ATATCCCATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.27
Consensus pattern (17 bp):
ACAATGTATCGATACAT
Found at i:20596 original size:19 final size:20
Alignment explanation
Indices: 20549--20597 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
20539 CACCCAGATA
20549 TATCAATACATATTGCTAAG
1 TATCAATACATATTGCTAAG
* * **
20569 TATCGATACATGTT-CTTGG
1 TATCAATACATATTGCTAAG
20588 TATCAATACA
1 TATCAATACA
20598 CACTAAATTG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (20 bp):
TATCAATACATATTGCTAAG
Found at i:20665 original size:13 final size:14
Alignment explanation
Indices: 20646--20682 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
20636 AACTCACTCA
20646 GTATCGATACAGTT
1 GTATCGATACAGTT
20660 -TATCGATAC-GTT
1 GTATCGATACAGTT
*
20672 GTATGGATACA
1 GTATCGATACA
20683 TGGTCAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
12 3 0.15
13 17 0.85
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.35
Consensus pattern (14 bp):
GTATCGATACAGTT
Found at i:21129 original size:23 final size:23
Alignment explanation
Indices: 21099--21142 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
21089 GCATTCAACC
21099 TTGGGGTACAATCTCTT-AAGAAT
1 TTGGGGTACAAT-TCTTGAAGAAT
*
21122 TTGGGGTATAATTCTTGAAGA
1 TTGGGGTACAATTCTTGAAGA
21143 GATTGAGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.30, C:0.09, G:0.25, T:0.36
Consensus pattern (23 bp):
TTGGGGTACAATTCTTGAAGAAT
Found at i:22303 original size:15 final size:15
Alignment explanation
Indices: 22283--22313 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
22273 TCAACCATCA
*
22283 ATGATGATGATGTTG
1 ATGATGATGAAGTTG
22298 ATGATGATGAAGTTG
1 ATGATGATGAAGTTG
22313 A
1 A
22314 CTCGAATGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (15 bp):
ATGATGATGAAGTTG
Done.