Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold60
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: 3815296
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 18690 characters in sequence are not A, C, G, or T
File 21 of 21
Found at i:3812305 original size:41 final size:42
Alignment explanation
Indices: 3812233--3812328 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 42
3812223 AAAACCCAAG
*
3812233 AACCCCAAAGTCTGCCTCAACCGCCAAA-CCCCGAAA-CGCCCA
1 AACCCCAAAG-CCGCCTCAACCGCCAAACCCCCGAAACCG-CCA
* *
3812275 AACCCCAAAGCCGCCAT-AACCGCCACACCCCCGAATCCGCCA
1 AACCCCAAAGCCGCC-TCAACCGCCAAACCCCCGAAACCGCCA
3812317 AAGCCCCAAAGC
1 AA-CCCCAAAGC
3812329 TCTCCCAAGC
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
41 13 0.28
42 23 0.49
43 11 0.23
ACGTcount: A:0.33, C:0.49, G:0.12, T:0.05
Consensus pattern (42 bp):
AACCCCAAAGCCGCCTCAACCGCCAAACCCCCGAAACCGCCA
Found at i:3812760 original size:6 final size:7
Alignment explanation
Indices: 3812707--3812867 Score: 99
Period size: 7 Copynumber: 20.0 Consensus size: 7
3812697 CTCGCCAGAG
3812707 CCCCAATA
1 CCCCAA-A
3812715 CCCCAAA
1 CCCCAAA
3812722 GCCCCAAAA
1 -CCCC-AAA
3812731 CGCCTCAATA
1 C-CC-CAA-A
3812741 CCCCAAA
1 CCCCAAA
3812748 CCCCAAA
1 CCCCAAA
*
3812755 CCCAAAAA
1 CCC-CAAA
3812763 CCCCAAA
1 CCCCAAA
3812770 CCCTCAAA
1 CCC-CAAA
3812778 CCCCAAA
1 CCCCAAA
3812785 CCCCATAAA
1 CCCC--AAA
3812794 CCCGCGAGAA
1 CCC-C-A-AA
3812804 CCCC-AA
1 CCCCAAA
3812810 CTCTCCGAGAA
1 C-C-CC-A-AA
3812821 CCCCAAA
1 CCCCAAA
*
3812828 CCCGAAA
1 CCCCAAA
3812835 CCCCAAAGA
1 CCCC-AA-A
3812844 CCCCGGGAAA
1 CCCC---AAA
3812854 CCCCAAA
1 CCCCAAA
3812861 CCCCAAA
1 CCCCAAA
3812868 TCCTCCAAAT
Statistics
Matches: 127, Mismatches: 6, Indels: 41
0.73 0.03 0.24
Matches are distributed among these distances:
6 3 0.02
7 48 0.38
8 32 0.25
9 24 0.19
10 15 0.12
11 5 0.04
ACGTcount: A:0.40, C:0.48, G:0.07, T:0.04
Consensus pattern (7 bp):
CCCCAAA
Found at i:3812765 original size:15 final size:14
Alignment explanation
Indices: 3812708--3812787 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 14
3812698 TCGCCAGAGC
*
3812708 CCCAATACCCCAAA
1 CCCAAAACCCCAAA
3812722 GCCCCAAAACGCCTCAATA
1 --CCCAAAAC-CC-CAA-A
*
3812741 CCCCAAACCCCAAA
1 CCCAAAACCCCAAA
3812755 CCCAAAAACCCCAAA
1 CCC-AAAACCCCAAA
*
3812770 CCCTCAAACCCCAAA
1 CCC-AAAACCCCAAA
3812785 CCC
1 CCC
3812788 CATAAACCCG
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
14 4 0.07
15 29 0.53
16 9 0.16
17 9 0.16
18 3 0.05
19 1 0.02
ACGTcount: A:0.41, C:0.51, G:0.03, T:0.05
Consensus pattern (14 bp):
CCCAAAACCCCAAA
Found at i:3812768 original size:22 final size:22
Alignment explanation
Indices: 3812740--3812789 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
3812730 ACGCCTCAAT
3812740 ACCCCAAACCC-CAAACCCAAAA
1 ACCCCAAACCCTCAAACCC-AAA
*
3812762 ACCCCAAACCCTCAAACCCCAA
1 ACCCCAAACCCTCAAACCCAAA
3812784 ACCCCA
1 ACCCCA
3812790 TAAACCCGCG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 19 0.73
23 7 0.27
ACGTcount: A:0.44, C:0.54, G:0.00, T:0.02
Consensus pattern (22 bp):
ACCCCAAACCCTCAAACCCAAA
Found at i:3813129 original size:7 final size:7
Alignment explanation
Indices: 3813107--3813228 Score: 57
Period size: 7 Copynumber: 15.3 Consensus size: 7
3813097 CTCTAGAACG
3813107 CCCAAAC
1 CCCAAAC
*
3813114 CGTCAAAC
1 C-CCAAAC
3813122 CCCAAAC
1 CCCAAAC
3813129 CCTCAGGAAC
1 CC-CA--AAC
*
3813139 CCACAATC
1 CC-CAAAC
3813147 CCCAAAC
1 CCCAAAC
3813154 CCCAAA-
1 CCCAAAC
3813160 CCCAAAC
1 CCCAAAC
3813167 GCCTCAAATC
1 -CC-CAAA-C
3813177 CGGCCAATAC
1 C--CCAA-AC
* *
3813187 CTCACTAC
1 CCCA-AAC
3813195 CCCAAAC
1 CCCAAAC
3813202 CCCAAAC
1 CCCAAAC
3813209 TCCCTATAGAC
1 -CCC-A-A-AC
3813220 CCCAAAC
1 CCCAAAC
3813227 CC
1 CC
3813229 TCTCAAACCT
Statistics
Matches: 90, Mismatches: 9, Indels: 32
0.69 0.07 0.24
Matches are distributed among these distances:
6 6 0.07
7 31 0.34
8 25 0.28
9 7 0.08
10 17 0.19
11 4 0.04
ACGTcount: A:0.36, C:0.49, G:0.06, T:0.09
Consensus pattern (7 bp):
CCCAAAC
Found at i:3813457 original size:7 final size:7
Alignment explanation
Indices: 3813436--3815294 Score: 1144
Period size: 7 Copynumber: 246.0 Consensus size: 7
3813426 AAAGACTACT
3813436 CAAACCC
1 CAAACCC
3813443 CTAAACCC
1 C-AAACCC
3813451 CAAACCC
1 CAAACCC
*
3813458 GCAATCCC
1 -CAAACCC
3813466 CAAACCC
1 CAAACCC
3813473 TCACCAACCC
1 -CA--AACCC
3813483 CAACACCC
1 CAA-ACCC
3813491 CAATACTCC
1 CAA-AC-CC
*
3813500 CACAATCC
1 CA-AACCC
3813508 CATAACCC
1 CA-AACCC
3813516 CGTATTAACCC
1 C--A--AACCC
3813527 CGAAACCCC
1 C-AAA-CCC
3813536 CAACACGCC
1 CAA-AC-CC
**
3813545 ACACCCCC
1 -CAAACCC
3813553 CAAACCC
1 CAAACCC
3813560 CAAAACCC
1 C-AAACCC
3813568 CAAACTCC
1 CAAAC-CC
3813576 TCAAACCC
1 -CAAACCC
*
3813584 AAAAACCC
1 -CAAACCC
***
3813592 C-CTTCC
1 CAAACCC
*
3813598 AAAACCCC
1 CAAA-CCC
3813606 CAAACCC
1 CAAACCC
3813613 CAAACCC
1 CAAACCC
3813620 CAAACCCC
1 CAAA-CCC
*
3813628 CCAA-CC
1 CAAACCC
3813634 CAAACCC
1 CAAACCC
3813641 CAAACCC
1 CAAACCC
3813648 CTAAATCCC
1 C-AAA-CCC
3813657 CAAACCC
1 CAAACCC
3813664 CAAGACCCTC
1 CAA-A-CC-C
3813674 CAAACGCC
1 CAAAC-CC
3813682 CAAGACCC
1 CAA-ACCC
3813690 CAAAGCCC
1 CAAA-CCC
3813698 CAATACCC
1 CAA-ACCC
3813706 TCAGAACCTC
1 -CA-AACC-C
3813716 CAGAA-CC
1 CA-AACCC
3813723 CAAACCC
1 CAAACCC
3813730 CATAAGACCC
1 C--AA-ACCC
3813740 CAAACCC
1 CAAACCC
3813747 CAGATACTCC
1 CA-A-AC-CC
*
3813757 CAAATCC
1 CAAACCC
3813764 CAACACCC
1 CAA-ACCC
*
3813772 C-AACCT
1 CAAACCC
3813778 CAAAGCCC
1 CAAA-CCC
3813786 CAAACCC
1 CAAACCC
3813793 CAAACTCC
1 CAAAC-CC
3813801 CAAACCTCC
1 CAAA-C-CC
3813810 CAAAACCC
1 C-AAACCC
3813818 CAAAATCCC
1 C-AAA-CCC
3813827 CAAAACCC
1 C-AAACCC
3813835 CAATTACCTC
1 CAA--ACC-C
3813845 CAGAACCC
1 CA-AACCC
3813853 CAAACCC
1 CAAACCC
3813860 CAAACCC
1 CAAACCC
3813867 CAAACCC
1 CAAACCC
3813874 CTAAACCC
1 C-AAACCC
3813882 CAAAACTCC
1 C-AAAC-CC
3813891 CAAACGCC
1 CAAAC-CC
3813899 C-AACCC
1 CAAACCC
*
3813905 CAAAACC
1 CAAACCC
3813912 CAATACCC
1 CAA-ACCC
*
3813920 TAAACGCC
1 CAAAC-CC
3813928 CAAACCTC
1 CAAACC-C
3813936 CAAAACCC
1 C-AAACCC
*
3813944 CAACTCCC
1 CAA-ACCC
3813952 TCAAACCC
1 -CAAACCC
3813960 CTTTATATACCC
1 C---A-A-ACCC
*
3813972 TCAAATTCCG
1 -CAAA--CCC
3813982 CAAACTCC
1 CAAAC-CC
3813990 TCAAACCC
1 -CAAACCC
3813998 CAAAATCCC
1 C-AAA-CCC
3814007 TCATAAACTCC
1 -C--AAAC-CC
3814018 CAAACCC
1 CAAACCC
3814025 CAAACCCC
1 CAAA-CCC
*
3814033 CACACCCC
1 CA-AACCC
3814041 CATAACCTC
1 CA-AACC-C
3814050 CGATAATCCC
1 C-A-AA-CCC
3814060 TCTAAACCC
1 -C-AAACCC
3814069 CAATTATCTGCCC
1 CAA--A----CCC
3814082 CAAACCC
1 CAAACCC
3814089 CAAAACTCC
1 C-AAAC-CC
3814098 TCATATA-CC
1 -CA-A-ACCC
*
3814107 CATACTTTCTCC
1 CA-A---AC-CC
3814119 CAAATCTCC
1 CAAA-C-CC
3814128 CAAACCTC
1 CAAACC-C
3814136 TCAAACCC
1 -CAAACCC
3814144 CAAACCC
1 CAAACCC
**
3814151 CCCA-CC
1 CAAACCC
3814157 CAAACCC
1 CAAACCC
3814164 CAAACCC
1 CAAACCC
3814171 C-AACCC
1 CAAACCC
3814177 CAAACCC
1 CAAACCC
3814184 CAAA-CC
1 CAAACCC
3814190 CAAACCC
1 CAAACCC
*
3814197 CCAACCC
1 CAAACCC
3814204 CAATACCC
1 CAA-ACCC
*
3814212 CCAACCC
1 CAAACCC
3814219 CAAACCC
1 CAAACCC
3814226 CAAACCC
1 CAAACCC
*
3814233 CACACCCC
1 CA-AACCC
*
3814241 CAACCCC
1 CAAACCC
*
3814248 CTTCAACCC
1 C--AAACCC
3814257 CAAACCC
1 CAAACCC
3814264 CAAACTCC
1 CAAAC-CC
3814272 CAAACCC
1 CAAACCC
*
3814279 AAAACCC
1 CAAACCC
3814286 CAAACCC
1 CAAACCC
3814293 CAAATCCC
1 CAAA-CCC
3814301 C-AACCC
1 CAAACCC
*
3814307 CCAACCC
1 CAAACCC
3814314 CAAACCC
1 CAAACCC
3814321 CAAACCC
1 CAAACCC
3814328 CAACACCC
1 CAA-ACCC
*
3814336 C--CCCC
1 CAAACCC
3814341 CAACACCC
1 CAA-ACCC
3814349 CTAATACCC
1 C-AA-ACCC
*
3814358 TCACACCC
1 -CAAACCC
3814366 CAAACTCC
1 CAAAC-CC
3814374 CGAAA-CC
1 C-AAACCC
3814381 CAAACCC
1 CAAACCC
3814388 CAAAATCCC
1 C-AAA-CCC
3814397 CAAACCC
1 CAAACCC
3814404 CAAACCC
1 CAAACCC
3814411 CAAACCC
1 CAAACCC
3814418 CAAACCC
1 CAAACCC
3814425 CAAACCC
1 CAAACCC
3814432 CAAACCC
1 CAAACCC
3814439 CAACACCC
1 CAA-ACCC
3814447 CAAACCC
1 CAAACCC
3814454 C-AA--C
1 CAAACCC
3814458 CAAACCC
1 CAAACCC
*
3814465 CACACCC
1 CAAACCC
3814472 CAAA-CC
1 CAAACCC
3814478 CAAACCC
1 CAAACCC
3814485 CAAATTACCC
1 C-AA--ACCC
3814495 CAAACCCC
1 CAAA-CCC
3814503 CAAATCCC
1 CAAA-CCC
*
3814511 CCAACCTC
1 CAAACC-C
3814519 CAAACCC
1 CAAACCC
3814526 CAAACCC
1 CAAACCC
3814533 CAAACCC
1 CAAACCC
3814540 CAAAACCC
1 C-AAACCC
3814548 CAAACCC
1 CAAACCC
3814555 TCAAACCC
1 -CAAACCC
3814563 C-AACCC
1 CAAACCC
3814569 CAAACCC
1 CAAACCC
3814576 CAAACCC
1 CAAACCC
3814583 CAAACCC
1 CAAACCC
3814590 CAAACCC
1 CAAACCC
3814597 CTATAACCC
1 C-A-AACCC
3814606 CAAACCC
1 CAAACCC
*
3814613 TCACACCTC
1 -CAAACC-C
3814622 CAAACCC
1 CAAACCC
3814629 CAAAACCC
1 C-AAACCC
3814637 CAACACCC
1 CAA-ACCC
3814645 CAAACCC
1 CAAACCC
3814652 CAAA-CC
1 CAAACCC
3814658 CAGAACTCC
1 CA-AAC-CC
3814667 CAAACCC
1 CAAACCC
3814674 CAAAACCC
1 C-AAACCC
3814682 CAAACCC
1 CAAACCC
3814689 CAAACCC
1 CAAACCC
3814696 CAAA-CC
1 CAAACCC
3814702 CAGAACCC
1 CA-AACCC
3814710 C-AACCC
1 CAAACCC
3814716 CAAACCC
1 CAAACCC
*
3814723 CAAACCT
1 CAAACCC
*
3814730 CAAAACC
1 CAAACCC
3814737 CAAA-CC
1 CAAACCC
3814743 CAAACCC
1 CAAACCC
3814750 C-AACCC
1 CAAACCC
3814756 CAAACCC
1 CAAACCC
3814763 CAAAACCC
1 C-AAACCC
3814771 CAAACCC
1 CAAACCC
3814778 CAAACCC
1 CAAACCC
*
3814785 CAACCCC
1 CAAACCC
3814792 CAAAACCCC
1 C-AAA-CCC
3814801 CAAACCC
1 CAAACCC
3814808 CAAACCC
1 CAAACCC
3814815 CAAACCC
1 CAAACCC
3814822 CAAACCC
1 CAAACCC
3814829 CAAA-CC
1 CAAACCC
3814835 CAATACCC
1 CAA-ACCC
3814843 CAAACCCC
1 CAAA-CCC
3814851 TCAAACCC
1 -CAAACCC
3814859 CAAAACCC
1 C-AAACCC
3814867 CAAACCC
1 CAAACCC
3814874 CAAACCC
1 CAAACCC
3814881 CAAACCC
1 CAAACCC
3814888 CAAACCC
1 CAAACCC
3814895 CAAAACCC
1 C-AAACCC
3814903 CAAACCC
1 CAAACCC
3814910 CAAAAACCC
1 C--AAACCC
3814919 CAAACCC
1 CAAACCC
*
3814926 CTAACCCC
1 C-AAACCC
3814934 CAAACCC
1 CAAACCC
3814941 CAAAAACCC
1 C--AAACCC
3814950 CAAATCCC
1 CAAA-CCC
3814958 CAAACCCC
1 CAAA-CCC
*
3814966 CACACCC
1 CAAACCC
3814973 C-AA-CC
1 CAAACCC
3814978 CAAACCC
1 CAAACCC
3814985 C---CCC
1 CAAACCC
***
3814989 CTTCCCC
1 CAAACCC
***
3814996 CTCCCCC
1 CAAACCC
***
3815003 CCTCCCC
1 CAAACCC
3815010 CAAACCC
1 CAAACCC
***
3815017 CCCCCCC
1 CAAACCC
***
3815024 CCCCCCC
1 CAAACCC
***
3815031 CCCCCCC
1 CAAACCC
***
3815038 CCCCCCC
1 CAAACCC
***
3815045 CCCTCCC
1 CAAACCC
*
3815052 C-CACCC
1 CAAACCC
***
3815058 CCCCCCC
1 CAAACCC
***
3815065 CCCCCCC
1 CAAACCC
*
3815072 TCCAACCC
1 -CAAACCC
3815080 CAAACCC
1 CAAACCC
3815087 CAAACCC
1 CAAACCC
*
3815094 TAAAACCC
1 -CAAACCC
*
3815102 TAAAACCC
1 -CAAACCC
* *
3815110 TAAAACC
1 CAAACCC
*
3815117 GAAACCC
1 CAAACCC
*
3815124 TAAACCC
1 CAAACCC
*
3815131 TAAACCC
1 CAAACCC
3815138 CTAAAAACCC
1 C---AAACCC
3815148 CAAACCC
1 CAAACCC
*
3815155 TAAAACCC
1 -CAAACCC
3815163 CAAACCC
1 CAAACCC
3815170 CAAACCC
1 CAAACCC
3815177 CAAACCC
1 CAAACCC
*
3815184 CCAACCC
1 CAAACCC
3815191 C-AACCC
1 CAAACCC
*
3815197 CACACCC
1 CAAACCC
3815204 CAAAACCC
1 C-AAACCC
3815212 CAAAAACCC
1 C--AAACCC
3815221 CATAACCC
1 CA-AACCC
3815229 CAAACCC
1 CAAACCC
3815236 C-AA-CC
1 CAAACCC
*
3815241 CAAAACC
1 CAAACCC
3815248 CAAACCC
1 CAAACCC
*
3815255 CTATA--C
1 C-AAACCC
*
3815261 AAAACCC
1 CAAACCC
*
3815268 CAAA-AC
1 CAAACCC
*
3815274 CTAACCC
1 CAAACCC
*
3815281 CTAACCC
1 CAAACCC
3815288 CAAACCC
1 CAAACCC
3815295 TA
Statistics
Matches: 1548, Mismatches: 118, Indels: 372
0.76 0.06 0.18
Matches are distributed among these distances:
4 6 0.00
5 14 0.01
6 107 0.07
7 720 0.47
8 426 0.28
9 178 0.11
10 61 0.04
11 21 0.01
12 8 0.01
13 7 0.00
ACGTcount: A:0.38, C:0.55, G:0.01, T:0.06
Consensus pattern (7 bp):
CAAACCC
Found at i:3813629 original size:36 final size:35
Alignment explanation
Indices: 3813522--3813664 Score: 124
Period size: 36 Copynumber: 3.8 Consensus size: 35
3813512 ACCCCGTATT
* *
3813522 AACCCCGAAACCCCCAACACGCCACACCCCCCAAACCCCAA
1 AACCCC-AAA-CCCCAA-ACCCCAAACCCCCC-AA--CCAA
* * **
3813563 AACCCCAAACTCCTCAAACCCAAAAACCCCCTTCCAA
1 AACCCCAAAC-CC-CAAACCCCAAACCCCCCAACCAA
*
3813600 AACCCCCAAACCCCAAACCCCAAACCCCCCAACCCA
1 AA-CCCCAAACCCCAAACCCCAAACCCCCCAACCAA
3813636 AACCCCAAACCCCTAAATCCCCAAACCCC
1 AACCCCAAACCCC-AAA-CCCCAAACCCC
3813665 AAGACCCTCC
Statistics
Matches: 86, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
35 11 0.13
36 23 0.27
37 19 0.22
38 8 0.09
39 1 0.01
40 15 0.17
41 9 0.10
ACGTcount: A:0.38, C:0.56, G:0.01, T:0.04
Consensus pattern (35 bp):
AACCCCAAACCCCAAACCCCAAACCCCCCAACCAA
Found at i:3813635 original size:28 final size:29
Alignment explanation
Indices: 3813436--3814985 Score: 1016
Period size: 29 Copynumber: 50.3 Consensus size: 29
3813426 AAAGACTACT
* *
3813436 CAAACCCCTAAACCCCAAACCCGCAATCCC
1 CAAACCCC-AAACCCCAAACCCCCAAACCC
3813466 CAAACCCTCACCAACCCC-AACACCCCAATACTCC
1 CAAACCC-CA--AACCCCAAAC-CCCCAA-AC-CC
* *
3813500 CACAATCCCATAACCCCGTATTAACCCCGAAACCCC
1 CA-AACCCCA-AACCCC--A--AACCCCCAAA-CCC
** *
3813536 CAACACGCCACACCCCCCAAACCCCAAAACCC
1 CAA-AC-CC-CAAACCCCAAACCCCCAAACCC
* **
3813568 CAAACTCCTCAAACCCAAAAACCCCC--TTCC
1 CAAAC-CC-CAAACCC-CAAACCCCCAAACCC
*
3813598 AAAACCCCCAAACCCCAAA-CCCCAAACCCC
1 CAAA-CCCCAAACCCCAAACCCCCAAA-CCC
* *
3813628 CCAA-CCCAAACCCCAAACCCCTAAATCCC
1 CAAACCCCAAACCCCAAACCCCCAAA-CCC
*
3813657 CAAACCCCAAGACCCTCCAAACGCCCAAGACCC
1 CAAACCCCAA-A-CC-CCAAACCCCCAA-ACCC
*
3813690 CAAAGCCCCAATACCCTCAGAACCTCCAGAA-CC
1 CAAA-CCCCAA-ACCC-CA-AACCCCCA-AACCC
3813723 CAAACCCCATAAGACCCCAAA-CCCCAGATACTCC
1 CAAACCCC--AA-ACCCCAAACCCCCA-A-AC-CC
* *
3813757 CAAATCCCAACACCCC-AA-CCTCAAAGCCC
1 CAAACCCCAA-ACCCCAAACCCCCAAA-CCC
3813786 CAAACCCCAAACTCCCAAACCTCCCAAAACCC
1 CAAACCCCAAAC-CCCAAACC-CCC-AAACCC
*
3813818 CAAAATCCCCAAAACCCCAATTACCTCCAGAACCC
1 C-AAA-CCCC-AAACCCCAA--ACCCCCA-AACCC
*
3813853 CAAACCCCAAACCCCAAACCCCTAAACCC
1 CAAACCCCAAACCCCAAACCCCCAAACCC
*
3813882 CAAAACTCCCAAACGCCC-AA-CCCCAAAACC
1 C-AAAC-CCCAAAC-CCCAAACCCCCAAACCC
* *
3813912 CAATACCCTAAACGCCCAAACCTCCAAAACCC
1 CAA-ACCCCAAAC-CCCAAACC-CCCAAACCC
* * *
3813944 CAACTCCCTCAAACCCCTTTATATACCCTCAAATTCCG
1 CAA-ACCC-CAAACCCC---A-A-ACCCCCAAA--CCC
*
3813982 CAAACTCCTCAAACCCCAAAATCCCTCATAAACTCC
1 CAAAC-CC-CAAACCCC-AAA-CCC-C-CAAAC-CC
*
3814018 CAAACCCCAAACCCCCACACCCCCATAACCTC
1 CAAACCCCAAA-CCCCAAACCCCCA-AACC-C
3814050 CGATAATCCCTCTAAACCCCAATTATCTGCCCCAAACCC
1 C-A-AA-CCC-C-AAACCCCAA--A-C--CCCCAAACCC
*
3814089 CAAAACTCCTCATATA-CCCATACTTTCTCCCAAATCTCC
1 C-AAAC-CC-CA-A-ACCCCAAAC---C-CCCAAA-C-CC
3814128 CAAACCTCTCAAACCCCAAACCCCCCACCCAAACCC
1 CAAACC-C-CAAACCCCAAA----CC-CCCAAACCC
3814164 CAAACCCC-AACCCCAAA-CCCCAAA-CC
1 CAAACCCCAAACCCCAAACCCCCAAACCC
*
3814190 CAAACCCCCAACCCCAATACCCCC-AACCC
1 CAAACCCCAAACCCCAA-ACCCCCAAACCC
* *
3814219 CAAACCCCAAACCCCACACCCCCAACCCC
1 CAAACCCCAAACCCCAAACCCCCAAACCC
** * * *
3814248 CTTCAACCCCAAACCCCAAACTCCCAAACCC
1 C-AAACCCCA-AACCCCAAACCCCCAAACCC
* *
3814279 AAAACCCCAAACCCCAAATCCCC-AACCC
1 CAAACCCCAAACCCCAAACCCCCAAACCC
*
3814307 CCAACCCCAAACCCCAAA-CCCCAACACCC
1 CAAACCCCAAACCCCAAACCCCCAA-ACCC
* * *
3814336 C--CCCCCAACACCCCTAATACCCTCACACCC
1 CAAACCCCAA-ACCCC-AA-ACCCCCAAACCC
*
3814366 CAAACTCCCGAAA-CCCAAACCCCAAAATCCC
1 CAAAC-CCC-AAACCCCAAACCCCCAAA-CCC
3814397 CAAACCCCAAACCCCAAA-CCCCAAACCC
1 CAAACCCCAAACCCCAAACCCCCAAACCC
3814425 CAAACCCCAAACCCC-AACACCCCAAACCC
1 CAAACCCCAAACCCCAAAC-CCCCAAACCC
*
3814454 C-AA--CCAAACCCCACA-CCCCAAA-CC
1 CAAACCCCAAACCCCAAACCCCCAAACCC
*
3814478 CAAACCCCAAATTACCCCAAACCCCCAAATCCC
1 CAAACCCCAAA--CCCC-AAACCCCCAAA-CCC
*
3814511 CCAACCTCCAAACCCCAAA-CCCCAAACCC
1 CAAACC-CCAAACCCCAAACCCCCAAACCC
3814540 CAAAACCCCAAACCCTCAAA-CCCC-AACCC
1 C-AAACCCCAAACCC-CAAACCCCCAAACCC
3814569 CAAACCCCAAACCCCAAA-CCCCAAACCC
1 CAAACCCCAAACCCCAAACCCCCAAACCC
* *
3814597 CTATAACCCCAAACCCTCACACCTCCAAACCC
1 C-A-AACCCCAAACCC-CAAACCCCCAAACCC
3814629 CAAAACCCCAACACCCCAAA-CCCCAAA-CC
1 C-AAACCCCAA-ACCCCAAACCCCCAAACCC
*
3814658 CAGAACTCCCAAACCCCAAAACCCCAAACCC
1 CA-AAC-CCCAAACCCCAAACCCCCAAACCC
3814689 CAAACCCCAAA-CCCAGAA-CCCC-AACCC
1 CAAACCCCAAACCCCA-AACCCCCAAACCC
* *
3814716 CAAACCCCAAACCTCAAA-ACCCAAA-CC
1 CAAACCCCAAACCCCAAACCCCCAAACCC
*
3814743 CAAACCCC-AACCCCAAACCCCAAAACCC
1 CAAACCCCAAACCCCAAACCCCCAAACCC
3814771 CAAACCCCAAACCCC-AACCCCCAAAACCCC
1 CAAACCCCAAACCCCAAACCCCC-AAA-CCC
3814801 CAAACCCCAAACCCCAAA-CCCCAAACCC
1 CAAACCCCAAACCCCAAACCCCCAAACCC
3814829 CAAA-CCCAATACCCCAAACCCCTCAAACCC
1 CAAACCCCAA-ACCCCAAACCCC-CAAACCC
3814859 CAAAACCCCAAACCCCAAA-CCCCAAACCC
1 C-AAACCCCAAACCCCAAACCCCCAAACCC
*
3814888 CAAACCCCAAAACCCCAAACCCCAAAAACCC
1 CAAACCCC-AAACCCCAAACCCC-CAAACCC
* *
3814919 CAAACCCCTAACCCCCAAACCCCAAAAACCC
1 CAAACCCC-AAACCCCAAACCCC-CAAACCC
*
3814950 CAAATCCCCAAACCCC-CACACCCC-AA-CC
1 CAAA-CCCCAAACCCCAAAC-CCCCAAACCC
3814978 CAAACCCC
1 CAAACCCC
3814986 CCCCTTCCCC
Statistics
Matches: 1248, Mismatches: 115, Indels: 317
0.74 0.07 0.19
Matches are distributed among these distances:
24 3 0.00
25 9 0.01
26 27 0.02
27 89 0.07
28 152 0.12
29 196 0.16
30 171 0.14
31 160 0.13
32 112 0.09
33 83 0.07
34 66 0.05
35 36 0.03
36 39 0.03
37 38 0.03
38 49 0.04
39 8 0.01
40 4 0.00
41 6 0.00
ACGTcount: A:0.39, C:0.53, G:0.01, T:0.06
Consensus pattern (29 bp):
CAAACCCCAAACCCCAAACCCCCAAACCC
Found at i:3813685 original size:18 final size:17
Alignment explanation
Indices: 3813612--3813707 Score: 68
Period size: 16 Copynumber: 6.1 Consensus size: 17
3813602 CCCCCAAACC
3813612 CCAAACCCCAA-ACCC-
1 CCAAACCCCAAGACCCT
*
3813627 CCCAA-CCCAA-A-CC-
1 CCAAACCCCAAGACCCT
*
3813640 CCAAACCCCTAA-ATCC-
1 CCAAACCCC-AAGACCCT
3813656 CCAAACCCCAAGACCCT
1 CCAAACCCCAAGACCCT
3813673 CCAAACGCCCAAGA-CC-
1 CCAAAC-CCCAAGACCCT
*
3813689 CCAAAGCCCCAATACCCT
1 CCAAA-CCCCAAGACCCT
3813707 C
1 C
3813708 AGAACCTCCA
Statistics
Matches: 68, Mismatches: 4, Indels: 15
0.78 0.05 0.17
Matches are distributed among these distances:
13 6 0.09
14 9 0.13
15 9 0.13
16 25 0.37
17 11 0.16
18 8 0.12
ACGTcount: A:0.36, C:0.54, G:0.04, T:0.05
Consensus pattern (17 bp):
CCAAACCCCAAGACCCT
Found at i:3813717 original size:42 final size:38
Alignment explanation
Indices: 3813603--3814965 Score: 642
Period size: 38 Copynumber: 35.3 Consensus size: 38
3813593 CTTCCAAAAC
**
3813603 CCCCAAACCCCAAA-CCCCAAACCCCCCAA-C-CCAAA
1 CCCCAAACCCCAAAGCCCCAAACCCCAGAACCTCCAAA
* *
3813638 CCCCAAACCCCTAAATCCCCAAACCCCAAGACCCTCCAAA
1 CCCCAAACCCC-AAAGCCCCAAACCCC-AGAACCTCCAAA
3813678 CGCCCAAGACCCCAAAGCCCCAATACCCTCAGAACCTCCAGAA
1 C-CCCAA-ACCCCAAAGCCCCAA-ACCC-CAGAACCTCCA-AA
3813721 -CCCAAACCCCATAAGACCCCAAACCCCAGATA-CTCCCAAA
1 CCCCAAACCCCA-AAG-CCCCAAACCCCAGA-ACCT-CCAAA
*
3813761 TCCCAACACCCCAACCTCAAAGCCCCAAACCCCA-AA-CTCCCAAA
1 -CCC--CA----AACCCCAAAGCCCCAAACCCCAGAACCT-CCAAA
*
3813805 CCTCCCAAAACCCCAAAATCCCCAAAACCCCA-ATTACCTCCAGAA
1 -C-CCC-AAACCCC-AAAGCCCC-AAACCCCAGA--ACCTCCA-AA
3813850 CCCCAAACCCCAAA-CCCCAAACCCCTA-AACC-CCAAAA
1 CCCCAAACCCCAAAGCCCCAAACCCC-AGAACCTCC-AAA
* *
3813887 CTCCCAAACGCCC-AA-CCCCAAAACCCA-ATACC-CTAAA
1 C-CCCAAAC-CCCAAAGCCCCAAACCCCAGA-ACCTCCAAA
* *
3813924 CGCCCAAACCTCCAAAACCCCAACTCCCTCA-AACC-CCTTTATATA
1 C-CCCAAACC-CCAAAGCCCCAA-ACCC-CAGAACCTCC---A-A-A
* * *
3813969 CCCTCAAATTCCGCAAA-CTCCTCAAACCCCAAAATCCCTCATAAA
1 CCC-CAAA--CCCCAAAGC-CC-CAAACCCCAGAA--CCTC-CAAA
* * *
3814014 CTCCCAAACCCCAAACCCCCACACCCCCATAACCTCCGATAA
1 C-CCCAAACCCCAAAGCCCCA-AACCCCAGAACCTCC-A-AA
*
3814056 TCCCTCTAAACCCCAATTATCTGCCCCAAACCCCA-AAACTCCTCATATA
1 -CCC-C-AAACCCCAA--A---GCCCCAAACCCCAGAACCT-C-CA-A-A
* *
3814105 -CCCATACTTTCTCCCAAATCTCCCAAACCTCTCA-AACC-CCAAA
1 CCCCA-A---AC-CCCAAAGC-CCCAAACC-C-CAGAACCTCCAAA
**
3814148 CCCCCCA-CCCAAA-CCCCAAACCCC--AACC-CCAAA
1 CCCCAAACCCCAAAGCCCCAAACCCCAGAACCTCCAAA
* *
3814181 CCCCAAA-CCCAAA-CCCCCAACCCCA-ATACC-CCCAA
1 CCCCAAACCCCAAAGCCCCAAACCCCAGA-ACCTCCAAA
* * * *
3814216 CCCCAAACCCCAAA-CCCCACACCCC-CAACCCCCTTCAA
1 CCCCAAACCCCAAAGCCCCAAACCCCAGAACCTCC--AAA
*
3814254 CCCCAAACCCCAAA-CTCCCAAA-CCCAAAACC-CCAAA
1 CCCCAAACCCCAAAGC-CCCAAACCCCAGAACCTCCAAA
*
3814290 CCCCAAATCCCC-AA-CCCCCAACCCCA-AACC-CCAAA
1 CCCCAAA-CCCCAAAGCCCCAAACCCCAGAACCTCCAAA
* *
3814325 CCCCAACACCCC---CCCCCAACACCCCTA-ATACC-CTCACA
1 CCCCAA-ACCCCAAAGCCCCAA-ACCCC-AGA-ACCTC-CAAA
*
3814363 CCCCAAACTCCCGAAA--CCCAAACCCCAAAATCC-CCAAA
1 CCCCAAAC-CCC-AAAGCCCCAAACCCCAGAA-CCTCCAAA
3814401 CCCCAAACCCCAAA-CCCCAAACCCCA-AACC-CCAAA
1 CCCCAAACCCCAAAGCCCCAAACCCCAGAACCTCCAAA
* *
3814436 CCCCAACACCCCAAACCCCAACCAAACCCCA-CACC-CCAAA
1 CCCCAA-ACCCCAAA-GCC--CCAAACCCCAGAACCTCCAAA
* *
3814476 -CCCAAACCCCAAATTACCCCAAACCCCCA-AATCC-CCCAA
1 CCCCAAACCCCAAA--GCCCCAAA-CCCCAGAA-CCTCCAAA
*
3814515 CCTCCAAACCCCAAA-CCCCAAACCCCAAAACC-CCAAA
1 CC-CCAAACCCCAAAGCCCCAAACCCCAGAACCTCCAAA
3814552 CCCTCAAACCCC-AA-CCCCAAACCCCA-AACC-CCAAA
1 CCC-CAAACCCCAAAGCCCCAAACCCCAGAACCTCCAAA
*
3814587 CCCCAAACCCCTATAA-CCCCAAACCCTCA-CACCTCCAAA
1 CCCCAAACCCC-A-AAGCCCCAAACCC-CAGAACCTCCAAA
3814626 CCCCAAAACCCCAACA-CCCCAAACCCCA-AA-C-CCAGAA
1 CCCC-AAACCCCAA-AGCCCCAAACCCCAGAACCTCCA-AA
*
3814663 CTCCCAAACCCCAAAACCCCAAACCCCA-AACC-CCAAA
1 C-CCCAAACCCCAAAGCCCCAAACCCCAGAACCTCCAAA
3814700 -CCCAGAACCCC-AA-CCCCAAACCCCA-AACCT-CAAA
1 CCCCA-AACCCCAAAGCCCCAAACCCCAGAACCTCCAAA
*
3814734 ACCCAAA-CCCAAA-CCCC-AACCCCA-AACC-CCAAAA
1 CCCCAAACCCCAAAGCCCCAAACCCCAGAACCTCC-AAA
* * *
3814768 CCCCAAACCCCAAA-CCCCAACCCCCAAAACCCCCAAA
1 CCCCAAACCCCAAAGCCCCAAACCCCAGAACCTCCAAA
3814805 CCCCAAACCCCAAA-CCCCAAACCCCA-AA-C-CCAATA
1 CCCCAAACCCCAAAGCCCCAAACCCCAGAACCTCCAA-A
3814840 CCCCAAACCCCTCAAA-CCCCAAAACCCCA-AACC-CCAAA
1 CCCCAAA-CCC-CAAAGCCCC-AAACCCCAGAACCTCCAAA
3814878 CCCCAAACCCCAAA-CCCCAAAACCCCA-AACC-CCAAAAA
1 CCCCAAACCCCAAAGCCCC-AAACCCCAGAACCTCC--AAA
* * *
3814916 CCCCAAACCCCTAACCCCCAAACCCCAAAAACC-CCAAA
1 CCCCAAACCCCAAAGCCCCAAACCCC-AGAACCTCCAAA
3814954 TCCCCAAACCCC
1 -CCCCAAACCCC
3814966 CACACCCCAA
Statistics
Matches: 1123, Mismatches: 56, Indels: 294
0.76 0.04 0.20
Matches are distributed among these distances:
33 45 0.04
34 56 0.05
35 112 0.10
36 121 0.11
37 166 0.15
38 171 0.15
39 90 0.08
40 74 0.07
41 60 0.05
42 48 0.04
43 27 0.02
44 35 0.03
45 26 0.02
46 38 0.03
47 16 0.01
48 24 0.02
49 9 0.01
50 5 0.00
ACGTcount: A:0.39, C:0.53, G:0.01, T:0.06
Consensus pattern (38 bp):
CCCCAAACCCCAAAGCCCCAAACCCCAGAACCTCCAAA
Found at i:3813817 original size:88 final size:90
Alignment explanation
Indices: 3813762--3814965 Score: 407
Period size: 81 Copynumber: 14.2 Consensus size: 90
3813752 ACTCCCAAAT
*
3813762 CCCAACACCCC-AACCTCAAAGCCCC-AAACCCC-AAACTCCCAAACCTCCCAAAACCCCAAAAT
1 CCCAA-ACCCCAAACCCCAAA-CCCCTAAACCCCAAAACTCCCAAACCTCCCAAAACCCCAAAAT
3813824 CCCCAAAACCCCAATTACCTCCAGAAC
64 CCCCAAAACCCCAATTACCTCCAGAAC
*
3813851 CCCAAACCCCAAACCCCAAACCCCTAAACCCCAAAACTCCCAAA-CGCCC--AACCCCAAAA--C
1 CCCAAACCCCAAACCCCAAACCCCTAAACCCCAAAACTCCCAAACCTCCCAAAACCCCAAAATCC
* *
3813911 CCAATACCCTAA--ACGC-CCA-AAC
66 CCAAAACCCCAATTAC-CTCCAGAAC
* *
3813933 CTCCAAAACCCCAACTCCCTCAAACCCCTTTATATACCCTC-AAATTCCGCAAA-CTCCTC-AAA
1 C-CC-AAACCCCAA-ACCC-CAAACCCC--TA-A-ACCC-CAAAACTCC-CAAACCTCC-CAAAA
3813995 CCCCAAAATCCCTCATAAACTCCCAA--ACC-CCA-AACC
55 CCCCAAAATCCC-CA-AAAC-CCCAATTACCTCCAGAA-C
* *
3814031 CCCACACCCCCATAACCTCCGATAATCCCTCTAAACCCCAATTATCTGCCCCAAA-C-CCCAAAA
1 CCCA-AACCCCA-AACC-CC-A-AA-CCC-CTAAACCCCAA--AACT--CCCAAACCTCCCAAAA
* * **
3814094 CTCCTC-ATATACCCATACTTTCTCCCAAATCTCCCAAACCTCTCA-AAC
55 C-CC-CAAAATCCCCA-A--AAC-CCC-AAT-T-----ACCTC-CAGAAC
**
3814142 CCCAAACCCCCCA-CCCAAACCCC-AAACCCC--AAC-CCCAAA-C-CCC-AAA-CCC-AAA-CC
1 CCCAAACCCCAAACCCCAAACCCCTAAACCCCAAAACTCCCAAACCTCCCAAAACCCCAAAATCC
* *
3814196 CC-CAACCCCAA-TACC-CC-CAAC
66 CCAAAACCCCAATTACCTCCAGAAC
* * * **
3814217 CCCAAACCCCAAACCCCACACCCCCAACCCCCTTCAAC-CCCAAA-C-CCC-AAACTCCC-AAA-
1 CCCAAACCCCAAACCCCAAACCCCTAAACCCC-AAAACTCCCAAACCTCCCAAAAC-CCCAAAAT
3814276 -CCCAAAACCCCAA--ACC-CCA-AATC
64 CCCCAAAACCCCAATTACCTCCAGAA-C
* * * *
3814299 CCC-AACCCCCAACCCCAAACCCC-AAACCCCAACAC-CCC---CC-CCCAACACCCC-TAATAC
1 CCCAAACCCCAAACCCCAAACCCCTAAACCCCAAAACTCCCAAACCTCCCAAAACCCCAAAAT-C
* * *
3814356 CCTC-ACACCCCAA--A-CTCCCGAAA
65 CC-CAAAACCCCAATTACCTCCAGAAC
3814379 CCCAAACCCCAAAATCCCCAAACCCC-AAACCCC-AAAC-CCCAAA-C-CCC-AAACCCC-AAA-
1 CCCAAACCCC-AAA-CCCCAAACCCCTAAACCCCAAAACTCCCAAACCTCCCAAAACCCCAAAAT
* *** *
3814436 CCCCAACACCCCAAACCCCAACCA-AAC
64 CCCCAAAACCCCAATTACC-TCCAGAAC
* * *
3814463 CCCACACCCCAAA-CCCAAACCCCAAATTACCCC-AAACCCCCAAATCC-CCC--AACCTCC-AA
1 CCCAAACCCCAAACCCCAAACCCCTAA--ACCCCAAAACTCCCAAA-CCTCCCAAAACC-CCAAA
*
3814522 A-CCCC-AAACCCCAA--ACC-CCAAAAC
62 ATCCCCAAAACCCCAATTACCTCCAGAAC
*
3814546 CCCAAACCCTCAAACCCC-AACCCC-AAACCCC-AAAC-CCCAAA-C-CCC-AAACCCCTATAA-
1 CCCAAACCC-CAAACCCCAAACCCCTAAACCCCAAAACTCCCAAACCTCCCAAAACCCC-AAAAT
*
3814603 CCCC-AAACCCTC-A-CACCTCCA-AAC
64 CCCCAAAACCC-CAATTACCTCCAGAAC
*
3814627 CCCAAAACCCCAACACCCCAAACCCC-AAA-CCCAGAACTCCCAAA-C-CCCAAAACCCC-AAA-
1 CCC-AAACCCCAA-ACCCCAAACCCCTAAACCCCAAAACTCCCAAACCTCCCAAAACCCCAAAAT
3814686 CCCC-AAACCCCAA--A-C-CCAGAAC
64 CCCCAAAACCCCAATTACCTCCAGAAC
* *
3814708 CCC-AACCCCAAACCCCAAACCTC-AAAACCC-AAA--CCCAAA-C-CCC--AACCCC-AAA-CC
1 CCCAAACCCCAAACCCCAAACCCCTAAACCCCAAAACTCCCAAACCTCCCAAAACCCCAAAATCC
3814762 CCAAAACCCCAA--ACC-CCA-AAC
66 CCAAAACCCCAATTACCTCCAGAAC
* *
3814783 CCCAACCCCCAAAACCCCCAAACCCC-AAACCCC-AAAC-CCCAAA-C-CCC-AAA-CCCAATA-
1 CCCAAACCCC-AAA-CCCCAAACCCCTAAACCCCAAAACTCCCAAACCTCCCAAAACCCCAAAAT
* *
3814840 CCCCAAACCCCTCAA--ACC-CCAAAAC
64 CCCCAAAACCC-CAATTACCTCCAGAAC
*
3814865 CCCAAACCCCAAACCCCAAACCCC-AAACCCCAAAAC-CCCAAACC-CCAAAAACCCC-AAA-CC
1 CCCAAACCCCAAACCCCAAACCCCTAAACCCCAAAACTCCCAAACCTCCCAAAACCCCAAAATCC
* * *
3814925 CCTAACCCCCAA--ACC-CCAAAAAC
66 CCAAAACCCCAATTACCTCC-AGAAC
3814948 CCCAAATCCCCAAACCCC
1 CCCAAA-CCCCAAACCCC
3814966 CACACCCCAA
Statistics
Matches: 926, Mismatches: 68, Indels: 247
0.75 0.05 0.20
Matches are distributed among these distances:
74 13 0.01
75 31 0.03
76 29 0.03
77 21 0.02
78 44 0.05
79 34 0.04
80 93 0.10
81 110 0.12
82 78 0.08
83 100 0.11
84 73 0.08
85 35 0.04
86 21 0.02
87 23 0.02
88 11 0.01
89 25 0.03
90 24 0.03
91 11 0.01
92 3 0.00
93 10 0.01
94 3 0.00
95 12 0.01
96 4 0.00
97 25 0.03
98 15 0.02
99 16 0.02
100 15 0.02
101 9 0.01
102 9 0.01
103 1 0.00
104 3 0.00
105 2 0.00
106 1 0.00
107 2 0.00
108 1 0.00
109 1 0.00
110 8 0.01
111 6 0.01
112 4 0.00
ACGTcount: A:0.39, C:0.54, G:0.01, T:0.06
Consensus pattern (90 bp):
CCCAAACCCCAAACCCCAAACCCCTAAACCCCAAAACTCCCAAACCTCCCAAAACCCCAAAATCC
CCAAAACCCCAATTACCTCCAGAAC
Found at i:3813914 original size:45 final size:45
Alignment explanation
Indices: 3813842--3813947 Score: 135
Period size: 45 Copynumber: 2.3 Consensus size: 45
3813832 CCCCAATTAC
* *
3813842 CTCCAGAACCCCAAACCCCAAACCCCAA-ACCCCTAAAC-CCCAAAA
1 CTCCAAAACCCC-AACCCCAAAACCCAATA-CCCTAAACGCCCAAAA
* *
3813887 CTCCCAAACGCCCAACCCCAAAACCCAATACCCTAAACGCCCAAAC
1 CTCCAAAAC-CCCAACCCCAAAACCCAATACCCTAAACGCCCAAAA
3813933 CTCCAAAACCCCAAC
1 CTCCAAAACCCCAAC
3813948 TCCCTCAAAC
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
45 35 0.66
46 18 0.34
ACGTcount: A:0.41, C:0.51, G:0.03, T:0.06
Consensus pattern (45 bp):
CTCCAAAACCCCAACCCCAAAACCCAATACCCTAAACGCCCAAAA
Found at i:3814988 original size:1 final size:1
Alignment explanation
Indices: 3814982--3815071 Score: 99
Period size: 1 Copynumber: 90.0 Consensus size: 1
3814972 CCAACCCAAA
** * * ***
3814982 CCCCCCCCTTCCCCCTCCCCCCCTCCCCCAAACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
* *
3815047 CTCCCCCACCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
3815072 TCCAACCCCA
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
1 77 1.00
ACGTcount: A:0.04, C:0.90, G:0.00, T:0.06
Consensus pattern (1 bp):
C
Found at i:3815030 original size:43 final size:41
Alignment explanation
Indices: 3814982--3815071 Score: 135
Period size: 43 Copynumber: 2.1 Consensus size: 41
3814972 CCAACCCAAA
** *
3814982 CCCCCCCCTTCCCCCTCCCCCCCTCCCCCAAACCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCTCCCCC--ACCCCCCCCCCC
3815025 CCCCCCCCCCCCCCCCCCCCCCCTCCCCCACCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCTCCCCCACCCCCCCCCCC
3815066 CCCCCC
1 CCCCCC
3815072 TCCAACCCCA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
41 18 0.41
43 26 0.59
ACGTcount: A:0.04, C:0.90, G:0.00, T:0.06
Consensus pattern (41 bp):
CCCCCCCCCCCCCCCCCCCCCCCTCCCCCACCCCCCCCCCC
Found at i:3815031 original size:35 final size:34
Alignment explanation
Indices: 3814982--3815087 Score: 106
Period size: 34 Copynumber: 3.1 Consensus size: 34
3814972 CCAACCCAAA
** * *
3814982 CCCCCCCCTTCCCCCTCCCCCCCTCCCCCAAACC
1 CCCCCCCCCCCCCCCCCCCCCCCACCCCCAAACC
***
3815016 CCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCTC
1 CCCCCCCCCCCCCCCCCCCCCCCACCCCCAAAC-C
*
3815050 CCCCACCCCCCCCCCCCCCCCCTCCAACCCCAAACC
1 CCCC-CCCCCCCCCCCCCCCCC-CCACCCCCAAACC
3815086 CC
1 CC
3815088 AAACCCTAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
33 6 0.10
34 25 0.43
35 17 0.29
36 5 0.09
37 5 0.09
ACGTcount: A:0.08, C:0.86, G:0.00, T:0.06
Consensus pattern (34 bp):
CCCCCCCCCCCCCCCCCCCCCCCACCCCCAAACC
Found at i:3815058 original size:22 final size:22
Alignment explanation
Indices: 3814992--3815069 Score: 115
Period size: 22 Copynumber: 3.6 Consensus size: 22
3814982 CCCCCCCCTT
* *
3814992 CCCCCTCCCCCCCTCCCCCAAAC
1 CCCCCCCCCCCCCTCCCCC-ACC
3815015 CCCCCCCCCCCCC-CCCCC-CC
1 CCCCCCCCCCCCCTCCCCCACC
3815035 CCCCCCCCCCCCCTCCCCCACC
1 CCCCCCCCCCCCCTCCCCCACC
3815057 CCCCCCCCCCCCC
1 CCCCCCCCCCCCC
3815070 CCTCCAACCC
Statistics
Matches: 51, Mismatches: 2, Indels: 5
0.88 0.03 0.09
Matches are distributed among these distances:
20 14 0.27
21 5 0.10
22 20 0.39
23 12 0.24
ACGTcount: A:0.05, C:0.91, G:0.00, T:0.04
Consensus pattern (22 bp):
CCCCCCCCCCCCCTCCCCCACC
Found at i:3815087 original size:27 final size:27
Alignment explanation
Indices: 3815029--3815087 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
3815019 CCCCCCCCCC
** * *
3815029 CCCCCCCCCCCCCCCCCCCTCCCCCAC
1 CCCCCCCCCCCCCCCCCCAACCCCAAA
3815056 CCCCCCCCCCCCCCCCTCCAACCCCAAA
1 CCCCCCCCCCCCCCCC-CCAACCCCAAA
3815084 CCCC
1 CCCC
3815088 AAACCCTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 16 0.59
28 11 0.41
ACGTcount: A:0.10, C:0.86, G:0.00, T:0.03
Consensus pattern (27 bp):
CCCCCCCCCCCCCCCCCCAACCCCAAA
Found at i:3815248 original size:58 final size:56
Alignment explanation
Indices: 3815075--3815255 Score: 175
Period size: 58 Copynumber: 3.1 Consensus size: 56
3815065 CCCCCCCTCC
* * * * * * *
3815075 AACCCCAAACCCCAAACCCTAAAACCCTAAAACCCTAAAACCGAAACCCTAAACCCTA
1 AACCCCACACCCCAAACCCAAAAACCC-CAAACCCCAAACCCCAAACCCAAAACCC-A
* * ** *
3815133 AACCCCTAAAAACCCCAAACCCTAAAACCCCAAACCCCAAACCCCAAACCCCCAACCCC
1 AACCCC---ACACCCCAAACCCAAAAACCCCAAACCCCAAACCCCAAACCCAAAACCCA
3815192 AACCCCACACCCCAAAACCCCAAAAACCCCATAACCCCAAACCCC-AACCCAAAACCCA
1 AACCCCACACCCC-AAA-CCCAAAAACCCCA-AACCCCAAACCCCAAACCCAAAACCCA
3815250 AACCCC
1 AACCCC
3815256 TATACAAAAC
Statistics
Matches: 105, Mismatches: 12, Indels: 12
0.81 0.09 0.09
Matches are distributed among these distances:
56 6 0.06
57 3 0.03
58 34 0.32
59 19 0.18
60 22 0.21
61 21 0.20
ACGTcount: A:0.44, C:0.51, G:0.01, T:0.04
Consensus pattern (56 bp):
AACCCCACACCCCAAACCCAAAAACCCCAAACCCCAAACCCCAAACCCAAAACCCA
Found at i:3815263 original size:19 final size:19
Alignment explanation
Indices: 3815227--3815267 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3815217 ACCCCATAAC
*
3815227 CCCAAACCCCAACCCAAAA
1 CCCAAACCCCAACACAAAA
* *
3815246 CCCAAACCCCTATACAAAA
1 CCCAAACCCCAACACAAAA
3815265 CCC
1 CCC
3815268 CAAAACCTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.51, G:0.00, T:0.05
Consensus pattern (19 bp):
CCCAAACCCCAACACAAAA
Done.