Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 132 of 240
Found at i:40938779 original size:22 final size:22
Alignment explanation
Indices: 40938723--40938781 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
40938713 AATAAAATTG
*
40938723 AAATATTAAATAATT-TATTAAC
1 AAATA-TAAATAATTATATGAAC
* *
40938745 AAAT-TATACTAATTATATGAAT
1 AAATATA-AATAATTATATGAAC
40938767 AAATATAAATAATTA
1 AAATATAAATAATTA
40938782 AATATGTATG
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
20 2 0.07
21 6 0.20
22 20 0.67
23 2 0.07
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (22 bp):
AAATATAAATAATTATATGAAC
Found at i:40941493 original size:33 final size:32
Alignment explanation
Indices: 40941456--40941560 Score: 111
Period size: 33 Copynumber: 3.2 Consensus size: 32
40941446 GAAGGAAAGG
* * *
40941456 GAGAGAGAAAGAAGAGAAAAAGATAAGGAGAAA
1 GAGAG-GAAAGAAGAGAGAAGGAAAAGGAGAAA
* * *
40941489 GAGAGGGATAGGAGAGAGAAGGAAAAGGAGAGA
1 GAGA-GGAAAGAAGAGAGAAGGAAAAGGAGAAA
**
40941522 GAGAGGAGGGAAAGAGAGAAGGAAAAGGAGAAA
1 GAGAGGAAAG-AAGAGAGAAGGAAAAGGAGAAA
40941555 GAGAGG
1 GAGAGG
40941561 GAGATAGACC
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
32 4 0.07
33 55 0.92
34 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.44, T:0.02
Consensus pattern (32 bp):
GAGAGGAAAGAAGAGAGAAGGAAAAGGAGAAA
Found at i:40941517 original size:66 final size:66
Alignment explanation
Indices: 40941425--40941562 Score: 161
Period size: 66 Copynumber: 2.1 Consensus size: 66
40941415 ATTTAGAGAG
* * * * *
40941425 GAGGGGTAGCAGAGAGAGGGAGAAGGAAAGGGAGAGAGAAAG-AAGAGAAAAAGATAAGGAGAAA
1 GAGGGATAGCAGAGAGAAGGAAAAGGAAAGAGAGAG-GAAAGAAAGAGAAAAAGAAAAGGAGAAA
40941489 GA
65 GA
* * ** * *
40941491 GAGGGATAGGAGAGAGAAGGAAAAGGAGAGAGAGAGGAGGGAAAGAGAGAAGGAAAAGGAGAAAG
1 GAGGGATAGCAGAGAGAAGGAAAAGGAAAGAGAGAGGAAAGAAAGAGAAAAAGAAAAGGAGAAAG
40941556 A
66 A
40941557 GAGGGA
1 GAGGGA
40941563 GATAGACCGG
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
65 3 0.05
66 57 0.95
ACGTcount: A:0.51, C:0.01, G:0.46, T:0.02
Consensus pattern (66 bp):
GAGGGATAGCAGAGAGAAGGAAAAGGAAAGAGAGAGGAAAGAAAGAGAAAAAGAAAAGGAGAAAG
A
Found at i:40941554 original size:20 final size:20
Alignment explanation
Indices: 40941501--40941559 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
40941491 GAGGGATAGG
40941501 AGAGAGAAGGAAAAGGAG--
1 AGAGAGAAGGAAAAGGAGAA
40941519 AGAGAG-AGG---AGG-GAA
1 AGAGAGAAGGAAAAGGAGAA
40941534 AGAGAGAAGGAAAAGGAGAA
1 AGAGAGAAGGAAAAGGAGAA
40941554 AGAGAG
1 AGAGAG
40941560 GGAGATAGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
13 1 0.03
14 3 0.09
15 6 0.18
16 3 0.09
17 3 0.09
18 6 0.18
19 3 0.09
20 9 0.26
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (20 bp):
AGAGAGAAGGAAAAGGAGAA
Found at i:40941650 original size:75 final size:76
Alignment explanation
Indices: 40941571--40941784 Score: 335
Period size: 75 Copynumber: 2.9 Consensus size: 76
40941561 GAGATAGACC
40941571 GGAGAGAGAGAAGCAGTAGTAGGTCGAGGAGGCACGAAAGTGATCGTGA-CATAGAGAGGGAACG
1 GGAGAGAGAGAAGCAGTAGTAGGTCGAGGAGGCACGAAAGTGATCGTGAGCATAGAGAGGGAACG
40941635 GGAGAGAGATA
66 GGAGAGAGATA
* * *
40941646 GGAGAGAGAGGAGCAGTAGTAGGTCGAGGAGGCACGAGAGTGATCGTGAGC-TAGAGAGGGAGCG
1 GGAGAGAGAGAAGCAGTAGTAGGTCGAGGAGGCACGAAAGTGATCGTGAGCATAGAGAGGGAACG
40941710 GGAGAGAGATA
66 GGAGAGAGATA
* * * * *
40941721 GGAGAGAGAGAAGCAGTAGTAGGTTGAGGAGACACGAAAGTGAACGCGATCA-AGAGAGGGAACG
1 GGAGAGAGAGAAGCAGTAGTAGGTCGAGGAGGCACGAAAGTGATCGTGAGCATAGAGAGGGAACG
40941785 TGAAATTGAC
Statistics
Matches: 126, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
75 125 0.99
76 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.44, T:0.10
Consensus pattern (76 bp):
GGAGAGAGAGAAGCAGTAGTAGGTCGAGGAGGCACGAAAGTGATCGTGAGCATAGAGAGGGAACG
GGAGAGAGATA
Found at i:40945191 original size:32 final size:32
Alignment explanation
Indices: 40945145--40945214 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
40945135 TTGAGCTTTT
40945145 ATGTTCATTATCCTGTATAGTAATAACCATGC
1 ATGTTCATTATCCTGTATAGTAATAACCATGC
*
40945177 ATGTTCATTTTCCTGTATAGTAATAACCATGC
1 ATGTTCATTATCCTGTATAGTAATAACCATGC
40945209 ATGTTC
1 ATGTTC
40945215 TTTGTTGGCC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.40
Consensus pattern (32 bp):
ATGTTCATTATCCTGTATAGTAATAACCATGC
Found at i:40947804 original size:20 final size:19
Alignment explanation
Indices: 40947750--40947805 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 19
40947740 ATCAAACTTC
*
40947750 TTTAAAAA-ATAAAACAAA
1 TTTAAAAATATAAAAAAAA
*
40947768 TTTACAAAATTACAAAAAAAA
1 TTTA-AAAA-TATAAAAAAAA
40947789 TTATAAAAATATAAAAA
1 TT-TAAAAATATAAAAA
40947806 GTACTAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 4 0.13
19 4 0.13
20 7 0.23
21 14 0.45
22 2 0.06
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (19 bp):
TTTAAAAATATAAAAAAAA
Found at i:40948666 original size:21 final size:21
Alignment explanation
Indices: 40948640--40948693 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
40948630 TCCCCTGCAC
*
40948640 TTCTACTGATACTTTGACAGG
1 TTCTACTGATACTCTGACAGG
*
40948661 TTCTACTGATACTCTGACGGG
1 TTCTACTGATACTCTGACAGG
*
40948682 TTCTACCGATAC
1 TTCTACTGATAC
40948694 CAAATGGAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (21 bp):
TTCTACTGATACTCTGACAGG
Found at i:40950462 original size:41 final size:41
Alignment explanation
Indices: 40950417--40950520 Score: 145
Period size: 41 Copynumber: 2.5 Consensus size: 41
40950407 GAGTGTATAT
* * *
40950417 AGGGGCACGTATGTGCAATTCAGGGGTACCGAAGTACGAAC
1 AGGGGCACGCATGTGCAATTCAGGGGTACCAAAGTACAAAC
** * *
40950458 AGGGGCATACATGTGCAATTTAGGGGTACTAAAGTACAAAC
1 AGGGGCACGCATGTGCAATTCAGGGGTACCAAAGTACAAAC
40950499 AGGGGCACGCATGTGCAATTCA
1 AGGGGCACGCATGTGCAATTCA
40950521 TACAATAATT
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.32, C:0.18, G:0.31, T:0.19
Consensus pattern (41 bp):
AGGGGCACGCATGTGCAATTCAGGGGTACCAAAGTACAAAC
Found at i:40963357 original size:24 final size:24
Alignment explanation
Indices: 40963324--40963369 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
40963314 AAATAGCGTG
* *
40963324 AAGTTTTTCATTTATTTTTTGCCA
1 AAGTTCTTCATTTAGTTTTTGCCA
40963348 AAGTTCTTCATTTAGTTTTTGC
1 AAGTTCTTCATTTAGTTTTTGC
40963370 TTCAATCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.20, C:0.13, G:0.11, T:0.57
Consensus pattern (24 bp):
AAGTTCTTCATTTAGTTTTTGCCA
Found at i:40965436 original size:45 final size:45
Alignment explanation
Indices: 40965372--40965462 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
40965362 TCAGCACTGC
*
40965372 ATTTCATCCTCAGACAGATGGCCAATCTGAGCGTGTAATTTAGGT
1 ATTTCATCCTCAGACAGATGGCCAATCTGAGCGTGTAATTCAGGT
40965417 ATTTCATCCTCAGACAGATGGCCAATCTGAGCGTGTAATTCAGGT
1 ATTTCATCCTCAGACAGATGGCCAATCTGAGCGTGTAATTCAGGT
40965462 A
1 A
40965463 CTGGAAGATA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (45 bp):
ATTTCATCCTCAGACAGATGGCCAATCTGAGCGTGTAATTCAGGT
Found at i:40967499 original size:14 final size:14
Alignment explanation
Indices: 40967480--40967507 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40967470 TTGAAAAATA
40967480 ATAAAAATAATTAG
1 ATAAAAATAATTAG
40967494 ATAAAAATAATTAG
1 ATAAAAATAATTAG
40967508 GGGCTTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (14 bp):
ATAAAAATAATTAG
Found at i:40970031 original size:12 final size:12
Alignment explanation
Indices: 40969993--40970082 Score: 51
Period size: 12 Copynumber: 7.5 Consensus size: 12
40969983 ATATACAAAC
40969993 TAATAT-AATAA
1 TAATATCAATAA
*
40970004 CAATATCAATAA
1 TAATATCAATAA
* *
40970016 TAATATCAGTAG
1 TAATATCAATAA
* ** *
40970028 TAATAACGGTGA
1 TAATATCAATAA
40970040 TAATAAT-AATAA
1 TAAT-ATCAATAA
*
40970052 TAA-ATTAATAA
1 TAATATCAATAA
*
40970063 TAATAGATTAATAA
1 TAAT--ATCAATAA
40970077 TAATAT
1 TAATAT
40970083 TACTGAATAG
Statistics
Matches: 61, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
10 2 0.03
11 13 0.21
12 33 0.54
13 1 0.02
14 12 0.20
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.33
Consensus pattern (12 bp):
TAATATCAATAA
Found at i:40970045 original size:3 final size:3
Alignment explanation
Indices: 40970039--40970081 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
40970029 AATAACGGTG
*
40970039 ATA ATA ATA ATA ATA A-A TTA ATA ATA ATA GATTA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -A-TA ATA ATA ATA
40970082 TTACTGAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 1 0.03
3 30 0.86
4 2 0.06
5 2 0.06
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:40970062 original size:14 final size:14
Alignment explanation
Indices: 40970043--40970081 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
40970033 ACGGTGATAA
40970043 TAATAATAATAAAT
1 TAATAATAATAAAT
*
40970057 TAATAATAATAGAT
1 TAATAATAATAAAT
40970071 TAATAATAATA
1 TAATAATAATA
40970082 TTACTGAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (14 bp):
TAATAATAATAAAT
Found at i:40970062 original size:17 final size:17
Alignment explanation
Indices: 40970039--40970081 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
40970029 AATAACGGTG
40970039 ATAATAATAATA-ATAA
1 ATAATAATAATAGATAA
*
40970055 ATTAATAATAATAGATTA
1 A-TAATAATAATAGATAA
40970073 ATAATAATA
1 ATAATAATA
40970082 TTACTGAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 1 0.04
17 19 0.79
18 4 0.17
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
ATAATAATAATAGATAA
Found at i:40980001 original size:15 final size:14
Alignment explanation
Indices: 40979974--40980004 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
40979964 GGACTCACAA
40979974 AAAAATAATAAACC
1 AAAAATAATAAACC
*
40979988 AAAAATAATAAAAC
1 AAAAATAATAAACC
40980002 AAA
1 AAA
40980005 GTCTAAGTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.10, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAAATAATAAACC
Found at i:40980156 original size:21 final size:19
Alignment explanation
Indices: 40980110--40980184 Score: 123
Period size: 19 Copynumber: 3.8 Consensus size: 19
40980100 AATCTTCAAG
40980110 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
40980129 GATATGCAATCTTAAATAT
1 GATATGCAATCTTAGATAT
40980148 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
40980169 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
40980185 AGATATAATT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
19 34 0.65
21 18 0.35
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:40980453 original size:23 final size:23
Alignment explanation
Indices: 40980409--40980453 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
40980399 TCTTATTTTG
* *
40980409 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
40980432 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
40980454 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:40980947 original size:23 final size:22
Alignment explanation
Indices: 40980918--40980961 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
40980908 ATAATTCACT
*
40980918 TACATATATATTTTTCTTATATG
1 TACATATATATATTT-TTATATG
40980941 TACATATATATATTTTTATAT
1 TACATATATATATTTTTATAT
40980962 TTTATAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (22 bp):
TACATATATATATTTTTATATG
Found at i:40998788 original size:16 final size:15
Alignment explanation
Indices: 40998767--40998797 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
40998757 TAATCAATCA
40998767 TGTAATGTACTAAATT
1 TGTAATGTAC-AAATT
40998783 TGTAATGTACAAATT
1 TGTAATGTACAAATT
40998798 CATATCATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (15 bp):
TGTAATGTACAAATT
Found at i:41000791 original size:21 final size:21
Alignment explanation
Indices: 41000765--41000808 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
41000755 CTATGCCTCG
*
41000765 AACTTCATCTCATAATGAGCC
1 AACTTCAACTCATAATGAGCC
**
41000786 AACTTCAACTTGTAATGAGCC
1 AACTTCAACTCATAATGAGCC
41000807 AA
1 AA
41000809 TAGCTTCAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.27
Consensus pattern (21 bp):
AACTTCAACTCATAATGAGCC
Found at i:41008096 original size:26 final size:26
Alignment explanation
Indices: 41008067--41008123 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
41008057 TACCAATGGA
* *
41008067 AAAATCGTTAAGATTTTACTAGGGGT
1 AAAATCGTTAAAATTTTACTAGAGGT
**
41008093 AAAATCGTTAAAATTTTGTTAGAGGT
1 AAAATCGTTAAAATTTTACTAGAGGT
41008119 AAAAT
1 AAAAT
41008124 AGGTATGAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.35
Consensus pattern (26 bp):
AAAATCGTTAAAATTTTACTAGAGGT
Found at i:41016461 original size:16 final size:18
Alignment explanation
Indices: 41016440--41016472 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
41016430 TATCTTTGAT
41016440 AAATT-ATTAT-TTTTTA
1 AAATTAATTATGTTTTTA
41016456 AAATTAATTATGTTTTT
1 AAATTAATTATGTTTTT
41016473 CTTAAATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
AAATTAATTATGTTTTTA
Found at i:41028702 original size:34 final size:34
Alignment explanation
Indices: 41028656--41028721 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
41028646 TGACCGCAAC
*
41028656 AACACTTCCATGCTAAAAATATTCAAACCCAAAT
1 AACACTTCCATGCTAAAAACATTCAAACCCAAAT
*
41028690 AACACTTTCATGCTAAAAACATTCAAACCCAA
1 AACACTTCCATGCTAAAAACATTCAAACCCAA
41028722 GTAAGATTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.47, C:0.27, G:0.03, T:0.23
Consensus pattern (34 bp):
AACACTTCCATGCTAAAAACATTCAAACCCAAAT
Found at i:41034030 original size:27 final size:27
Alignment explanation
Indices: 41034000--41034177 Score: 160
Period size: 27 Copynumber: 6.6 Consensus size: 27
41033990 TTATTGAGCC
* *
41034000 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
41034027 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
41034054 CGCACACTTAGTGCCACATAGTCCATCT
1 CGCACACTTAGTGCTACATAAT-CAACT
** ** *
41034082 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
41034109 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * * *
41034136 TGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
41034163 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41034178 GTACAATTTA
Statistics
Matches: 125, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
27 101 0.81
28 24 0.19
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:41034092 original size:55 final size:55
Alignment explanation
Indices: 41034000--41034176 Score: 191
Period size: 54 Copynumber: 3.3 Consensus size: 55
41033990 TTATTGAGCC
* * * * * *
41034000 CGCACACTCAGTGCTAT-ATAAT-CAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCCATCAT-ATCCATCTCGCACACTTAGTGCAACATAGTCAAAT
** * *
41034054 CGCACACTTAGTGCCA-CATAGTCCATCTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCCATCATA-TCCATCTCGCACACTTAGTGCAACATAGTCAAAT
* * *
41034109 CGCACACTTAGTG-CATCATATTCATTTTGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCCATCATATCCATCTCGCACACTTAGTGCAACATAGTCAAAT
41034163 CGCACACTTAGTGC
1 CGCACACTTAGTGC
41034177 TGTACAATTT
Statistics
Matches: 102, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
53 1 0.01
54 59 0.58
55 42 0.41
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (55 bp):
CGCACACTTAGTGCCATCATATCCATCTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:41041733 original size:46 final size:46
Alignment explanation
Indices: 41041658--41041770 Score: 172
Period size: 46 Copynumber: 2.4 Consensus size: 46
41041648 GCTGTAAACA
* *
41041658 AGACAAATTAAATTAGTTTAAGACAACTTAAATTCCTGTAATAATTT
1 AGACAAATTAAATGA-CTTAAGACAACTTAAATTCCTGTAATAATTT
* *
41041705 AGACAAATTAAATGACTTAAGACAACTTAAATTGCTGTAGTAATTT
1 AGACAAATTAAATGACTTAAGACAACTTAAATTCCTGTAATAATTT
*
41041751 AGATAAATTAAATGACTTAA
1 AGACAAATTAAATGACTTAA
41041771 CTTATTAATA
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
46 47 0.77
47 14 0.23
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.34
Consensus pattern (46 bp):
AGACAAATTAAATGACTTAAGACAACTTAAATTCCTGTAATAATTT
Found at i:41048376 original size:46 final size:47
Alignment explanation
Indices: 41048319--41048430 Score: 142
Period size: 46 Copynumber: 2.4 Consensus size: 47
41048309 GCTGTAAACA
* * * *
41048319 AGACAAATTAAATTG-TTTAAGACAACTTAAATTCCTGTA-ATAATTT
1 AGACAAATTAAATTGACTTAAGAAAACTTAAATTCCTATAGA-AATGT
*
41048365 AGACAAATTAAA-TGACTTAAGAAAACTTAAATTGCTATAGAAATGT
1 AGACAAATTAAATTGACTTAAGAAAACTTAAATTCCTATAGAAATGT
41048411 AGACAAATTAAA-TGACTTAA
1 AGACAAATTAAATTGACTTAA
41048431 CTTATTAATA
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
45 2 0.03
46 56 0.95
47 1 0.02
ACGTcount: A:0.48, C:0.10, G:0.11, T:0.31
Consensus pattern (47 bp):
AGACAAATTAAATTGACTTAAGAAAACTTAAATTCCTATAGAAATGT
Found at i:41054432 original size:29 final size:29
Alignment explanation
Indices: 41054400--41054456 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
41054390 AATTTTGATT
41054400 TTTTTAATATTTTGAT-GTATTTTTTTAAC
1 TTTTTAATATTTTGATAGT-TTTTTTTAAC
*
41054429 TTTTTAATATTTTTATAGTTTTTTTTAA
1 TTTTTAATATTTTGATAGTTTTTTTTAA
41054457 TTCGGGCTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (29 bp):
TTTTTAATATTTTGATAGTTTTTTTTAAC
Found at i:41055304 original size:14 final size:13
Alignment explanation
Indices: 41055283--41055320 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
41055273 GGAGAAGATG
41055283 AAAAAAGAAGA-AA
1 AAAAAAGAA-ATAA
41055296 AATAAAAGAAATAA
1 AA-AAAAGAAATAA
41055310 AAAAAAGAAAT
1 AAAAAAGAAAT
41055321 GGGGACATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.08
Consensus pattern (13 bp):
AAAAAAGAAATAA
Found at i:41057751 original size:31 final size:29
Alignment explanation
Indices: 41057708--41057769 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
41057698 TTTTATAAAT
*
41057708 AATTAATATTTAT-TAATTAAAAATATTTAC
1 AATTAATATTTATAT-ATT-AAAATATTAAC
*
41057738 AATTTATATTTTATATATTAAAATATTAAC
1 AATTAATA-TTTATATATTAAAATATTAAC
41057768 AA
1 AA
41057770 CAAGTTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 19 0.68
31 8 0.29
32 1 0.04
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (29 bp):
AATTAATATTTATATATTAAAATATTAAC
Found at i:41057955 original size:13 final size:12
Alignment explanation
Indices: 41057939--41057988 Score: 55
Period size: 13 Copynumber: 3.9 Consensus size: 12
41057929 TTTAAACTAA
41057939 ACTTTTCAAAAGC
1 ACTTTTCAAAA-C
*
41057952 ACTTCTCAAAATC
1 ACTTTTCAAAA-C
*
41057965 ACTTTTTCACAAC
1 AC-TTTTCAAAAC
41057978 ACTTTTCAAAA
1 ACTTTTCAAAA
41057989 ACAATGAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
12 8 0.26
13 16 0.52
14 7 0.23
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.34
Consensus pattern (12 bp):
ACTTTTCAAAAC
Found at i:41058235 original size:20 final size:19
Alignment explanation
Indices: 41058210--41058255 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
41058200 TTAATAATTC
41058210 TAATTTTTTAAACATTTTTA
1 TAATTTTTTAAA-ATTTTTA
*
41058230 TAATTTTTTTATAATTTTTA
1 TAA-TTTTTTAAAATTTTTA
41058250 -AATTTT
1 TAATTTT
41058256 AACAAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 4 0.17
19 2 0.08
20 10 0.42
21 8 0.33
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
TAATTTTTTAAAATTTTTA
Found at i:41058238 original size:11 final size:11
Alignment explanation
Indices: 41058224--41058248 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41058214 TTTTTAAACA
41058224 TTTTTATAATT
1 TTTTTATAATT
41058235 TTTTTATAATT
1 TTTTTATAATT
41058246 TTT
1 TTT
41058249 AAATTTTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTATAATT
Found at i:41058761 original size:23 final size:23
Alignment explanation
Indices: 41058735--41058779 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
41058725 AATTATATAT
41058735 ATTTTTTAATTTGTTAAATTTTA
1 ATTTTTTAATTTGTTAAATTTTA
* *
41058758 ATTTTTTATTTTTTTAAATTTT
1 ATTTTTTAATTTGTTAAATTTT
41058780 TATGAAGTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (23 bp):
ATTTTTTAATTTGTTAAATTTTA
Found at i:41058771 original size:8 final size:8
Alignment explanation
Indices: 41058720--41058781 Score: 54
Period size: 8 Copynumber: 7.8 Consensus size: 8
41058710 GATAGTTTTC
41058720 TTTTTAAT
1 TTTTTAAT
* *
41058728 TATATATAT
1 TTTTTA-AT
41058737 TTTTTAAT
1 TTTTTAAT
*
41058745 TTGTTAA-
1 TTTTTAAT
*
41058752 ATTTTAAT
1 TTTTTAAT
*
41058760 TTTTTATT
1 TTTTTAAT
*
41058768 TTTTTAAA
1 TTTTTAAT
41058776 TTTTTA
1 TTTTTA
41058782 TGAAGTACGT
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
7 5 0.12
8 30 0.73
9 6 0.15
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (8 bp):
TTTTTAAT
Found at i:41071077 original size:34 final size:33
Alignment explanation
Indices: 41071039--41071125 Score: 104
Period size: 34 Copynumber: 2.6 Consensus size: 33
41071029 TTTACAGTGT
*
41071039 TATTTGGTGTGATGGATGGATTAGCTTATACGA
1 TATTTGGTGTGATGGATGGATTAGCTCATACGA
*
41071072 GTATTTGGTGT-ACTGGATGAATTAGCTCATACGA
1 -TATTTGGTGTGA-TGGATGGATTAGCTCATACGA
* *
41071106 TCATCTGGTGTGCTGGATGG
1 T-ATTTGGTGTGATGGATGG
41071126 TTAACCGTGT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
33 2 0.04
34 43 0.96
ACGTcount: A:0.22, C:0.10, G:0.31, T:0.37
Consensus pattern (33 bp):
TATTTGGTGTGATGGATGGATTAGCTCATACGA
Found at i:41072089 original size:30 final size:31
Alignment explanation
Indices: 41072053--41072115 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 31
41072043 CAATTTTTTG
41072053 TCTGATTTGTTTCGATTT-GTCCCTGAATGT
1 TCTGATTTGTTTCGATTTGGTCCCTGAATGT
* *
41072083 TCTGATTTGTTTTGATTTGGTCCTTGAATGT
1 TCTGATTTGTTTCGATTTGGTCCCTGAATGT
41072114 TC
1 TC
41072116 CTAACCTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 17 0.57
31 13 0.43
ACGTcount: A:0.13, C:0.14, G:0.21, T:0.52
Consensus pattern (31 bp):
TCTGATTTGTTTCGATTTGGTCCCTGAATGT
Found at i:41081933 original size:20 final size:21
Alignment explanation
Indices: 41081908--41081963 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 21
41081898 TTCCTATGTT
*
41081908 ATTTTTATATTTGA-AAATTA
1 ATTTTTATATTTAATAAATTA
*
41081928 ATTTTT-TATTTAATAAATTT
1 ATTTTTATATTTAATAAATTA
* *
41081948 ATATTTATATATAATA
1 ATTTTTATATTTAATA
41081964 TTGTTTAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 6 0.20
20 16 0.53
21 8 0.27
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
ATTTTTATATTTAATAAATTA
Found at i:41088613 original size:13 final size:13
Alignment explanation
Indices: 41088597--41088634 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
41088587 TTTAAATCAA
41088597 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
41088610 ACTTTTTC-ACAGC
1 AC-TTTTCAAAAGC
41088623 ACTTTTCAAAAG
1 ACTTTTCAAAAG
41088635 TATTGCCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
12 5 0.24
13 11 0.52
14 5 0.24
ACGTcount: A:0.34, C:0.24, G:0.08, T:0.34
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:41089698 original size:9 final size:9
Alignment explanation
Indices: 41089672--41089753 Score: 56
Period size: 10 Copynumber: 8.4 Consensus size: 9
41089662 TTATACCATC
41089672 TTTTATGAAT
1 TTTTAT-AAT
* *
41089682 TCTAATAAT
1 TTTTATAAT
41089691 TTTTATAATT
1 TTTTATAA-T
*
41089701 TTTTACAAT
1 TTTTATAAT
*
41089710 ATTTTAGAAT
1 -TTTTATAAT
* *
41089720 TTGTAATAAA
1 TT-TTATAAT
41089730 TTTTATAGTAT
1 TTTTATA--AT
41089741 TTTTATAAT
1 TTTTATAAT
41089750 TTTT
1 TTTT
41089754 TACAATTTCT
Statistics
Matches: 56, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
9 22 0.39
10 26 0.46
11 8 0.14
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (9 bp):
TTTTATAAT
Found at i:41089699 original size:39 final size:39
Alignment explanation
Indices: 41089656--41089772 Score: 103
Period size: 39 Copynumber: 2.9 Consensus size: 39
41089646 AGAACTTTAA
* * *
41089656 ATAATTTTATACCATCTTTTATGAA-TTCTAATAATTTTT
1 ATAATTTTATACAATATTTTA-GAATTTCTAATAAATTTT
* *
41089695 ATAATTTTTTACAATATTTTAGAATTTGTAATAAATTTT
1 ATAATTTTATACAATATTTTAGAATTTCTAATAAATTTT
* * * *
41089734 ATAGTATTTT-TATAATTTTTTACAATTTCTTAAAAAATT
1 ATA--ATTTTATACAATATTTTAGAATTTC-TAATAAATT
41089773 ATAACATATT
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
38 3 0.05
39 33 0.52
40 15 0.23
41 13 0.20
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (39 bp):
ATAATTTTATACAATATTTTAGAATTTCTAATAAATTTT
Found at i:41089705 original size:10 final size:10
Alignment explanation
Indices: 41089686--41089761 Score: 57
Period size: 10 Copynumber: 7.7 Consensus size: 10
41089676 ATGAATTCTA
41089686 ATAA-TTTTT
1 ATAATTTTTT
41089695 ATAATTTTTT
1 ATAATTTTTT
* *
41089705 ACAATATTTT
1 ATAATTTTTT
* * *
41089715 AGAATTTGTA
1 ATAATTTTTT
*
41089725 ATAA-ATTTT
1 ATAATTTTTT
*
41089734 ATAGTATTTTT
1 ATAAT-TTTTT
41089745 ATAATTTTTT
1 ATAATTTTTT
*
41089755 ACAATTT
1 ATAATTT
41089762 CTTAAAAAAT
Statistics
Matches: 50, Mismatches: 14, Indels: 5
0.72 0.20 0.07
Matches are distributed among these distances:
9 9 0.18
10 33 0.66
11 8 0.16
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.58
Consensus pattern (10 bp):
ATAATTTTTT
Found at i:41089744 original size:40 final size:39
Alignment explanation
Indices: 41089684--41089761 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
41089674 TTATGAATTC
* *
41089684 TAATAATTTTTATAATTTTTTACAATATTTTAGAATTTG
1 TAATAAATTTTATAATTTTTTACAATATTTTACAATTTG
* * *
41089723 TAATAAATTTTATAGTATTTTTATAATTTTTTACAATTT
1 TAATAAATTTTATAAT-TTTTTACAATATTTTACAATTT
41089762 CTTAAAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 14 0.42
40 19 0.58
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.58
Consensus pattern (39 bp):
TAATAAATTTTATAATTTTTTACAATATTTTACAATTTG
Found at i:41089850 original size:20 final size:20
Alignment explanation
Indices: 41089822--41089863 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
41089812 TATAATTTTA
41089822 TTTACA-TTTTTTTGTGAATT
1 TTTACATTTTTTTTGT-AATT
*
41089842 TTTATATTTTTTTTGTAATT
1 TTTACATTTTTTTTGTAATT
41089862 TT
1 TT
41089864 AAAGATTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.19, C:0.02, G:0.07, T:0.71
Consensus pattern (20 bp):
TTTACATTTTTTTTGTAATT
Found at i:41099972 original size:5 final size:5
Alignment explanation
Indices: 41099962--41100028 Score: 107
Period size: 5 Copynumber: 12.8 Consensus size: 5
41099952 AGTTAACACA
41099962 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT
41100013 AAAAGT AAAAGT AAAA
1 AAAA-T AAAA-T AAAA
41100029 ACTATTTAGA
Statistics
Matches: 60, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
5 44 0.73
6 16 0.27
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:41112521 original size:21 final size:23
Alignment explanation
Indices: 41112497--41112544 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
41112487 TTTCGATCTC
41112497 TTTTTCTTT-TTCTCTC-ATTT-A
1 TTTTT-TTTCTTCTCTCAATTTCA
*
41112518 TTTTTTTTCTTTTCTCAATTTCA
1 TTTTTTTTCTTCTCTCAATTTCA
41112541 TTTT
1 TTTT
41112545 GGATTCGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 3 0.13
21 11 0.48
22 4 0.17
23 5 0.22
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTTTTTTCTTCTCTCAATTTCA
Found at i:41112543 original size:23 final size:24
Alignment explanation
Indices: 41112497--41112544 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
41112487 TTTCGATCTC
*
41112497 TTTTTCTTTTTCTCTCATTTATTT
1 TTTTTCTTTTTCTCTAATTTATTT
41112521 TTTTTC-TTTTCTC-AATTTCATTT
1 TTTTTCTTTTTCTCTAATTT-ATTT
41112544 T
1 T
41112545 GGATTCGTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 4 0.18
23 12 0.55
24 6 0.27
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTTTCTTTTTCTCTAATTTATTT
Found at i:41118511 original size:41 final size:41
Alignment explanation
Indices: 41118452--41118637 Score: 241
Period size: 41 Copynumber: 4.5 Consensus size: 41
41118442 TTTAAAATGA
* * * *
41118452 TTCACCGGCA-TATAGCCTGCTAGGCTTAAAGCCTG-ATTCAG
1 TTCACCGGCATTA-AGCCTGCTAGACGTAAAGTCTGAATT-AT
** * *
41118493 AACACCGGCATTAAGCCTGCTAGACGTAAAGTCTAAAATAT
1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTAT
*
41118534 TTCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAATTAT
1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTAT
*
41118575 TTCACTGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTAT
1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTAT
*
41118616 TTCACTGGCATTAAGCCTGCTA
1 TTCACCGGCATTAAGCCTGCTA
41118638 AGCACAGAGC
Statistics
Matches: 128, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
41 124 0.97
42 4 0.03
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (41 bp):
TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTAT
Found at i:41118842 original size:61 final size:61
Alignment explanation
Indices: 41118750--41118880 Score: 156
Period size: 61 Copynumber: 2.1 Consensus size: 61
41118740 ACATGAATAA
* * * *
41118750 ATATATATAATTCATAACACTAAGTTTAGCTCAAAGAACTTGTATA-TTACATTCGAACCTC
1 ATATATATAATTCAAAACACTAAATTTAGCTCAAAGAACTTGTA-ACCTACATTCGAACCAC
* * * * * *
41118811 ATATGTATAGTTCAAAACATTAAATTTAGCTCAATGAATTTGTAACCTATATTCGAACCAC
1 ATATATATAATTCAAAACACTAAATTTAGCTCAAAGAACTTGTAACCTACATTCGAACCAC
41118872 ATATATATA
1 ATATATATA
41118881 TAAATGTATA
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
60 1 0.02
61 57 0.98
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.35
Consensus pattern (61 bp):
ATATATATAATTCAAAACACTAAATTTAGCTCAAAGAACTTGTAACCTACATTCGAACCAC
Found at i:41123982 original size:12 final size:12
Alignment explanation
Indices: 41123965--41123989 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41123955 ATGAATAAAG
41123965 AATTAAAGAAAA
1 AATTAAAGAAAA
41123977 AATTAAAGAAAA
1 AATTAAAGAAAA
41123989 A
1 A
41123990 GATGATACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (12 bp):
AATTAAAGAAAA
Found at i:41125251 original size:54 final size:54
Alignment explanation
Indices: 41125187--41125457 Score: 281
Period size: 54 Copynumber: 5.0 Consensus size: 54
41125177 GTCTCAAACT
* * * *
41125187 GGTTGAGACACAAGCATGTAGACCAAGTCAGTGAGTTACACGGTCTGACACACA
1 GGTTGAGACACAGGCGTGTGGACCAAGTCAGTGAGTTACACGGTCTGACACACG
* * * * * * *
41125241 GGTTGGGACACAGGCGTATTGACCAATTCAATGAGTTACACGGTCTGGCACATG
1 GGTTGAGACACAGGCGTGTGGACCAAGTCAGTGAGTTACACGGTCTGACACACG
* * * * * * *
41125295 GGTTGAGACACAGGCATGTGGACCAAGTCTGTGAGTTGCATGATCTGGCACATG
1 GGTTGAGACACAGGCGTGTGGACCAAGTCAGTGAGTTACACGGTCTGACACACG
* * * ** * *
41125349 GGTTGAGACACGGGTGTGTCGACCAAGTTGGTGAGTTACACGATGTGACACACG
1 GGTTGAGACACAGGCGTGTGGACCAAGTCAGTGAGTTACACGGTCTGACACACG
* * * *
41125403 GGTTAAGACACGGGCGTGTGGACCAAGTCAGTGAGTTACACAGTTTGACACACG
1 GGTTGAGACACAGGCGTGTGGACCAAGTCAGTGAGTTACACGGTCTGACACACG
41125457 G
1 G
41125458 TTCGGTACAT
Statistics
Matches: 178, Mismatches: 39, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 178 1.00
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (54 bp):
GGTTGAGACACAGGCGTGTGGACCAAGTCAGTGAGTTACACGGTCTGACACACG
Found at i:41127853 original size:27 final size:26
Alignment explanation
Indices: 41127823--41127877 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 26
41127813 TAACATGAAA
*
41127823 GAATTCCTTGGTGGCAAACTCTGTAAG
1 GAATTCCTTCGTGGCAAACTCT-TAAG
*
41127850 GAATTCCTTCGTGGCACACTCTTAAG
1 GAATTCCTTCGTGGCAAACTCTTAAG
41127876 GA
1 GA
41127878 CCACCCTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 6 0.23
27 20 0.77
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (26 bp):
GAATTCCTTCGTGGCAAACTCTTAAG
Found at i:41130978 original size:26 final size:26
Alignment explanation
Indices: 41130944--41130998 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
41130934 TATACAAGAA
41130944 ATGTCTTTAACACCATTTAAAAAATC
1 ATGTCTTTAACACCATTTAAAAAATC
*
41130970 ATGTTTTTAACACCATTTAAAAAATC
1 ATGTCTTTAACACCATTTAAAAAATC
41130996 ATG
1 ATG
41130999 ACAATAGGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.36
Consensus pattern (26 bp):
ATGTCTTTAACACCATTTAAAAAATC
Found at i:41133900 original size:40 final size:41
Alignment explanation
Indices: 41133834--41133910 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 41
41133824 ACTTATGAAA
* *
41133834 TTCGAGATAGCTTTGGTTATTAATGGCACTTAGTGTGCGAT
1 TTCGAGATAGATTTGGCTATTAATGGCACTTAGTGTGCGAT
41133875 TTCGA-ATAGATTTGGCTA-TATATGGCACTTAGTGTG
1 TTCGAGATAGATTTGGCTATTA-ATGGCACTTAGTGTG
41133911 TGAAATTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 2 0.06
40 26 0.79
41 5 0.15
ACGTcount: A:0.23, C:0.12, G:0.26, T:0.39
Consensus pattern (41 bp):
TTCGAGATAGATTTGGCTATTAATGGCACTTAGTGTGCGAT
Found at i:41134715 original size:23 final size:23
Alignment explanation
Indices: 41134688--41134735 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
41134678 TGATTATTTC
41134688 GCATGTTACTATGATATTCAAAT
1 GCATGTTACTATGATATTCAAAT
41134711 GCATGTTACTATGATATTCAAAT
1 GCATGTTACTATGATATTCAAAT
41134734 GC
1 GC
41134736 GATTGTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (23 bp):
GCATGTTACTATGATATTCAAAT
Found at i:41134780 original size:24 final size:24
Alignment explanation
Indices: 41134753--41134837 Score: 125
Period size: 24 Copynumber: 3.5 Consensus size: 24
41134743 TTTACATGTT
*
41134753 TTAATGCTATCCATTTTGAGCATA
1 TTAATGCTGTCCATTTTGAGCATA
41134777 TTAATGCTGTCCATTTTGAGCATA
1 TTAATGCTGTCCATTTTGAGCATA
* * *
41134801 TTAATGATGTCAAGTTTGAGCATA
1 TTAATGCTGTCCATTTTGAGCATA
*
41134825 TGAATGCTGTCCA
1 TTAATGCTGTCCA
41134838 AAACAGATAA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (24 bp):
TTAATGCTGTCCATTTTGAGCATA
Found at i:41159924 original size:25 final size:25
Alignment explanation
Indices: 41159846--41159965 Score: 98
Period size: 25 Copynumber: 4.8 Consensus size: 25
41159836 TTATAGAGAG
* *
41159846 TTCGCCACAAAGGCTTTACAAAATA
1 TTCGCCACAAAGGCCTTACAGAATA
* * **** *
41159871 TTCACCAAAAATTATTTACAAAATA
1 TTCGCCACAAAGGCCTTACAGAATA
* *
41159896 TTCGCCACAAAGGCCTTATAGAGA-G
1 TTCGCCACAAAGGCCTTACAGA-ATA
**
41159921 TTCGCCACAAAGGTTTTACAGAATA
1 TTCGCCACAAAGGCCTTACAGAATA
*
41159946 TTCGCCACAAAGGCGTTACA
1 TTCGCCACAAAGGCCTTACA
41159966 AAGAGTTTTC
Statistics
Matches: 73, Mismatches: 20, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
24 1 0.01
25 71 0.97
26 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (25 bp):
TTCGCCACAAAGGCCTTACAGAATA
Found at i:41159983 original size:50 final size:50
Alignment explanation
Indices: 41159846--41159972 Score: 141
Period size: 50 Copynumber: 2.5 Consensus size: 50
41159836 TTATAGAGAG
* * * **
41159846 TTCGCCACAAAGGCTTTACAAA-ATATTCACCA-AAAATTATTTACAAAATA
1 TTCGCCACAAAGGCCTTACAAAGA-GTTCGCCACAAAGGT-TTTACAAAATA
* * *
41159896 TTCGCCACAAAGGCCTTATAGAGAGTTCGCCACAAAGGTTTTACAGAATA
1 TTCGCCACAAAGGCCTTACAAAGAGTTCGCCACAAAGGTTTTACAAAATA
*
41159946 TTCGCCACAAAGGCGTTACAAAGAGTT
1 TTCGCCACAAAGGCCTTACAAAGAGTT
41159973 TTCCATAAAG
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
50 59 0.92
51 5 0.08
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.25
Consensus pattern (50 bp):
TTCGCCACAAAGGCCTTACAAAGAGTTCGCCACAAAGGTTTTACAAAATA
Found at i:41162611 original size:19 final size:20
Alignment explanation
Indices: 41162587--41162624 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
41162577 AGAATTTTTT
41162587 TTATAAGCTTTTAT-AATAA
1 TTATAAGCTTTTATGAATAA
*
41162606 TTATAAGTTTTTATGAATA
1 TTATAAGCTTTTATGAATA
41162625 TTTTATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (20 bp):
TTATAAGCTTTTATGAATAA
Found at i:41162648 original size:18 final size:18
Alignment explanation
Indices: 41162625--41162691 Score: 57
Period size: 17 Copynumber: 3.7 Consensus size: 18
41162615 TTTATGAATA
41162625 TTTTATATATTTTTTTAG
1 TTTTATATATTTTTTTAG
* *
41162643 TTTTATAT-TTTTATAAG
1 TTTTATATATTTTTTTAG
***
41162660 -TTTATATAAACTTTTAG
1 TTTTATATATTTTTTTAG
41162677 TATATTATATATTTT
1 T-T-TTATATATTTT
41162692 AAATATATTG
Statistics
Matches: 35, Mismatches: 10, Indels: 6
0.69 0.20 0.12
Matches are distributed among these distances:
16 7 0.20
17 11 0.31
18 8 0.23
19 1 0.03
20 8 0.23
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.64
Consensus pattern (18 bp):
TTTTATATATTTTTTTAG
Found at i:41162829 original size:17 final size:17
Alignment explanation
Indices: 41162807--41162860 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 17
41162797 TTGATGTTAA
*
41162807 TAATTAATGGAGAAACT
1 TAATTAATAGAGAAACT
* *
41162824 TAATTAA-AGACAAA-A
1 TAATTAATAGAGAAACT
*
41162839 AAATTAATAGAGAAACT
1 TAATTAATAGAGAAACT
41162856 TAATT
1 TAATT
41162861 GAATTTATTT
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
15 6 0.21
16 11 0.39
17 11 0.39
ACGTcount: A:0.56, C:0.06, G:0.11, T:0.28
Consensus pattern (17 bp):
TAATTAATAGAGAAACT
Found at i:41164193 original size:19 final size:19
Alignment explanation
Indices: 41164131--41164200 Score: 65
Period size: 19 Copynumber: 3.6 Consensus size: 19
41164121 AGATCCCAAA
41164131 TATATTATTTTAGGAAATTTTT
1 TATATTA-TTTA-G-AATTTTT
41164153 TA-ATT-TTTA-ACATTTTT
1 TATATTATTTAGA-ATTTTT
41164170 ATATATTATTTAGAATTTTT
1 -TATATTATTTAGAATTTTT
*
41164190 TATAATATTTA
1 TATATTATTTA
41164201 TATTTGGTGG
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
16 1 0.02
17 6 0.14
18 2 0.05
19 17 0.40
20 10 0.24
21 4 0.10
22 2 0.05
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.60
Consensus pattern (19 bp):
TATATTATTTAGAATTTTT
Found at i:41164257 original size:18 final size:18
Alignment explanation
Indices: 41164236--41164273 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
41164226 GAATTGTTAT
41164236 AAAT-ATTTTGAGTTTTAA
1 AAATAATTTT-AGTTTTAA
*
41164254 AAATAATTTTATTTTTAA
1 AAATAATTTTAGTTTTAA
41164272 AA
1 AA
41164274 TTTTGAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
AAATAATTTTAGTTTTAA
Found at i:41184650 original size:15 final size:15
Alignment explanation
Indices: 41184619--41184655 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
41184609 AAAAAAAATT
41184619 TCGAGTT-AAACGAA
1 TCGAGTTAAAACGAA
*
41184633 TCGAGTTAAAATGAA
1 TCGAGTTAAAACGAA
41184648 TCGAGTTA
1 TCGAGTTA
41184656 TTTGAGTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.27
Consensus pattern (15 bp):
TCGAGTTAAAACGAA
Found at i:41184669 original size:18 final size:18
Alignment explanation
Indices: 41184646--41184680 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41184636 AGTTAAAATG
* *
41184646 AATCGAGTTATTTGAGTT
1 AATCGAATTATTCGAGTT
41184664 AATCGAATTATTCGAGT
1 AATCGAATTATTCGAGT
41184681 CAACTCAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (18 bp):
AATCGAATTATTCGAGTT
Found at i:41184986 original size:19 final size:20
Alignment explanation
Indices: 41184959--41184996 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41184949 CTCCCTTAAC
41184959 CTTCAAAA-CTTTTTATTTT
1 CTTCAAAACCTTTTTATTTT
*
41184978 CTTCCAAACCTTTTTATTT
1 CTTCAAAACCTTTTTATTT
41184997 CCCCCCTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.24, C:0.21, G:0.00, T:0.55
Consensus pattern (20 bp):
CTTCAAAACCTTTTTATTTT
Found at i:41190054 original size:129 final size:128
Alignment explanation
Indices: 41189817--41190076 Score: 346
Period size: 129 Copynumber: 2.0 Consensus size: 128
41189807 GAAAGTTACG
* **
41189817 AATTTAGTCATTGTACTTTAATTTGGTCATTTTTGGTCTCATATTTTTAAAATTTTTAAAATTTT
1 AATTTAGTCATTATACTTTAATTTGGTCATTTTTGGTCTCATATTTTTAAAATTTTTAAAATTGC
* * * * *
41189882 AATCATTAACAAACGGTAATTGTTTAATTTATTAAGTTCTATTATTT-TCAAATTTTGGTTGGGC
66 AA-CATGAACAAACGGTAATTGTTTAATTCATTAAATTCTATTATTTCT-AAAATTTGATTGGGC
* *
41189946 AATTTAGTCATTATACTTTAATTTGGTTATTTTTGGTCTCATATTTTTAAAA-TTTTAATCATTA
1 AATTTAGTCATTATACTTTAATTTGGTCATTTTTGGTCTCATATTTTTAAAATTTTTAA-AATT-
* *
41190010 GCAA-ATGAGCTAAACGGTAATTGTTTAATTCATTAAATTTTATTATTTCTAAAATTTGATTGGG
64 GCAACATGAAC-AAACGGTAATTGTTTAATTCATTAAATTCTATTATTTCTAAAATTTGATTGGG
41190074 C
128 C
41190075 AA
1 AA
41190077 ACATACTATC
Statistics
Matches: 115, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
128 10 0.09
129 102 0.89
130 3 0.03
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.49
Consensus pattern (128 bp):
AATTTAGTCATTATACTTTAATTTGGTCATTTTTGGTCTCATATTTTTAAAATTTTTAAAATTGC
AACATGAACAAACGGTAATTGTTTAATTCATTAAATTCTATTATTTCTAAAATTTGATTGGGC
Found at i:41190390 original size:28 final size:28
Alignment explanation
Indices: 41190331--41190390 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
41190321 TAAAATTTTA
*
41190331 AAATTCAAAAAGTAAATTAAAATGGACC
1 AAATTCAAAAAATAAATTAAAATGGACC
*
41190359 -AATTCAAAAAATATATTAAAAAT-GACC
1 AAATTCAAAAAATAAATT-AAAATGGACC
41190386 AAATT
1 AAATT
41190391 GAAGTATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 19 0.68
28 9 0.32
ACGTcount: A:0.58, C:0.10, G:0.07, T:0.25
Consensus pattern (28 bp):
AAATTCAAAAAATAAATTAAAATGGACC
Found at i:41191751 original size:11 final size:10
Alignment explanation
Indices: 41191724--41191761 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
41191714 GCACTTAACG
41191724 ATGTTTTT-T
1 ATGTTTTTAT
41191733 AGTGTTTTTAT
1 A-TGTTTTTAT
41191744 ATGTTTTTAT
1 ATGTTTTTAT
41191754 ATTGTTTT
1 A-TGTTTT
41191762 CGATTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 1 0.04
10 17 0.65
11 8 0.31
ACGTcount: A:0.16, C:0.00, G:0.13, T:0.71
Consensus pattern (10 bp):
ATGTTTTTAT
Found at i:41193813 original size:43 final size:43
Alignment explanation
Indices: 41193766--41193865 Score: 200
Period size: 43 Copynumber: 2.3 Consensus size: 43
41193756 AATCAAATTA
41193766 AATTATGTTCAAGTGTAATGGTTATCTATGTTAAATTCATATG
1 AATTATGTTCAAGTGTAATGGTTATCTATGTTAAATTCATATG
41193809 AATTATGTTCAAGTGTAATGGTTATCTATGTTAAATTCATATG
1 AATTATGTTCAAGTGTAATGGTTATCTATGTTAAATTCATATG
41193852 AATTATGTTCAAGT
1 AATTATGTTCAAGT
41193866 ATGCTAACAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (43 bp):
AATTATGTTCAAGTGTAATGGTTATCTATGTTAAATTCATATG
Found at i:41193817 original size:20 final size:20
Alignment explanation
Indices: 41193792--41193860 Score: 61
Period size: 20 Copynumber: 3.3 Consensus size: 20
41193782 AATGGTTATC
41193792 TATGTTAAATTCATATGAAT
1 TATGTTAAATTCATATGAAT
* *
41193812 TATGTTCAAGTGT-A-ATGGTTAT
1 TATGTT-AAAT-TCATAT-G-AAT
41193834 CTATGTTAAATTCATATGAAT
1 -TATGTTAAATTCATATGAAT
41193855 TATGTT
1 TATGTT
41193861 CAAGTATGCT
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
20 14 0.37
21 8 0.21
22 8 0.21
23 8 0.21
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.46
Consensus pattern (20 bp):
TATGTTAAATTCATATGAAT
Found at i:41195177 original size:31 final size:29
Alignment explanation
Indices: 41195120--41195177 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
41195110 TTCGAGCTTG
41195120 GGGAAAAAATGTAATTATGCAAAAGTTTA
1 GGGAAAAAATGTAATTATGCAAAAGTTTA
* *
41195149 GGGACAAAATCGTAATTTTGACAAAAGTT
1 GGGAAAAAAT-GTAATTATG-CAAAAGTT
41195178 GAGTCGAAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 9 0.36
30 8 0.32
31 8 0.32
ACGTcount: A:0.45, C:0.07, G:0.21, T:0.28
Consensus pattern (29 bp):
GGGAAAAAATGTAATTATGCAAAAGTTTA
Found at i:41195825 original size:102 final size:102
Alignment explanation
Indices: 41195649--41195979 Score: 389
Period size: 102 Copynumber: 3.3 Consensus size: 102
41195639 GATGAACATT
* *
41195649 TGTGTAGTACTGTGTGAAGGCTACTACGTGTATCAATAAATGATGGTCACATGTGTAGTACTAAG
1 TGTGTAGTACTGTGTGAAGGCTACTACGTGAATCAATAAATGATGGTCACATATGTAGTACTAAG
* *
41195714 TGAATGCTACAATGTGTACAGAGAAGCTTTGGTCACG
66 TGAAGGCTACAATGTGTACAGAAAAGCTTTGGTCACG
* * *
41195751 TGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATATGTATTAGTAAG
1 TGTGTAGTACTGTGTGAAGGCTACTACGTGAATCAATAAATGATGGTCACATATGTAGTACTAAG
* *
41195816 TGAAGGCTACTATGTGTACCGAAAAGCTTTGGTCACG
66 TGAAGGCTACAATGTGTACAGAAAAGCTTTGGTCACG
* * ** *** * * * *
41195853 TGTGTAGTACTATGTGAATGCTACTACGTGAA-CCGTAAAACTTGATCACGTGTGTAGTACTATG
1 TGTGTAGTACTGTGTGAAGGCTACTACGTGAATCAATAAATGATGGTCACATATGTAGTACTAAG
* ** * * *
41195917 TGAAGGCTACTACATGAACCGTAAAA-CTTT-ATCACG
66 TGAAGGCTACAATGTGTACAG-AAAAGCTTTGGTCACG
*
41195953 TGTGTAGTACTATGTGAAGGCTACTAC
1 TGTGTAGTACTGTGTGAAGGCTACTAC
41195980 ATGTATCGAA
Statistics
Matches: 201, Mismatches: 27, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
100 31 0.15
101 43 0.21
102 127 0.63
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (102 bp):
TGTGTAGTACTGTGTGAAGGCTACTACGTGAATCAATAAATGATGGTCACATATGTAGTACTAAG
TGAAGGCTACAATGTGTACAGAAAAGCTTTGGTCACG
Found at i:41195909 original size:50 final size:50
Alignment explanation
Indices: 41195649--41195979 Score: 306
Period size: 51 Copynumber: 6.5 Consensus size: 50
41195639 GATGAACATT
* * ** *** *
41195649 TGTGTAGTACTGTGTGAAGGCTACTACGTGTATCAATAAATGATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTG-AACCGTAAAACTTGGTCACG
* * * * * * *
41195700 TGTGTAGTACTAAGTGAATGCTACAATGTGTACAG-AGAAGCTTTGGTCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTA-AAAC-TTGGTCACG
* * *** *
41195751 TGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGGTCACG
* * * * * *
41195802 TATGTATTAGTAAGTGAAGGCTACTATGTGTACCG-AAAAGCTTTGGTCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAA-C-TTGGTCACG
* *
41195853 TGTGTAGTACTATGTGAATGCTACTACGTGAACCGTAAAACTTGATCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGTCACG
* **
41195903 TGTGTAGTACTATGTGAAGGCTACTACATGAACCGTAAAACTTTATCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGTCACG
41195953 TGTGTAGTACTATGTGAAGGCTACTAC
1 TGTGTAGTACTATGTGAAGGCTACTAC
41195980 ATGTATCGAA
Statistics
Matches: 226, Mismatches: 47, Indels: 15
0.78 0.16 0.05
Matches are distributed among these distances:
49 4 0.02
50 86 0.38
51 129 0.57
52 6 0.03
53 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (50 bp):
TGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGTCACG
Found at i:41206488 original size:50 final size:51
Alignment explanation
Indices: 41206311--41206503 Score: 203
Period size: 51 Copynumber: 3.8 Consensus size: 51
41206301 TTCCTATAAA
* * * * *
41206311 CACGTGTGTAGTACTAAGTGCAGGCTACTACGGGTATCG-ATAGATAATGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAAAGAT-TTGGT
* * * * *
41206362 CACATGTGTAGTACTATGTGCAGGCTATTATGTGTACC-AGAAGGCTTTGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGA-AAAGATTTGGT
* * * *
41206413 CACGTGCGTAGTACTATATGCAGGCTACTACGTGAACCGAAAAG-TTTGAT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAAAGATTTGGT
* *
41206463 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAA
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAA
41206504 TGATAATAAT
Statistics
Matches: 116, Mismatches: 23, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
50 41 0.35
51 71 0.61
52 4 0.03
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAAAGATTTGGT
Found at i:41206769 original size:36 final size:36
Alignment explanation
Indices: 41206722--41206794 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
41206712 AACAGAACAG
41206722 ATTCAAACACTGGAGGTGATGTTAGTTTCAAAAATC
1 ATTCAAACACTGGAGGTGATGTTAGTTTCAAAAATC
41206758 ATTCAAACACTGGAGGTGATGTTAGTTTCAAAAATC
1 ATTCAAACACTGGAGGTGATGTTAGTTTCAAAAATC
41206794 A
1 A
41206795 CCAAAAATTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (36 bp):
ATTCAAACACTGGAGGTGATGTTAGTTTCAAAAATC
Found at i:41213325 original size:32 final size:31
Alignment explanation
Indices: 41213280--41213375 Score: 165
Period size: 31 Copynumber: 3.1 Consensus size: 31
41213270 CTTAGATAAT
*
41213280 TTTAAAGAGTTTTATTAGGATTCAATTATTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
41213311 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
41213343 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
41213374 TT
1 TT
41213376 GTAATTTGCC
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 33 0.53
32 29 0.47
ACGTcount: A:0.31, C:0.08, G:0.14, T:0.47
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:41213971 original size:21 final size:20
Alignment explanation
Indices: 41213916--41213970 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
41213906 TTCTTTAAAT
41213916 AAAAA-CAAAAAAAACAGCAA
1 AAAAAGCAAAAAAAACA-CAA
* *
41213936 CAACAGCAAAAAAAACACAA
1 AAAAAGCAAAAAAAACACAA
41213956 AAAAAGCAAAAAAAA
1 AAAAAGCAAAAAAAA
41213971 AGCGCAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.78, C:0.16, G:0.05, T:0.00
Consensus pattern (20 bp):
AAAAAGCAAAAAAAACACAA
Found at i:41213979 original size:21 final size:20
Alignment explanation
Indices: 41213922--41213981 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
41213912 AAATAAAAAC
*
41213922 AAAAAAAACAGCAACAACAGCA
1 AAAAAAAAC-GCAA-AAAAGCA
*
41213944 AAAAAAACAC-AAAAAAAGCA
1 AAAAAAA-ACGCAAAAAAGCA
41213964 AAAAAAAAGCGCAAAAAA
1 AAAAAAAA-CGCAAAAAA
41213982 AGAGTAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 1 0.03
20 14 0.44
21 8 0.25
22 7 0.22
23 2 0.06
ACGTcount: A:0.75, C:0.17, G:0.08, T:0.00
Consensus pattern (20 bp):
AAAAAAAACGCAAAAAAGCA
Found at i:41214008 original size:11 final size:11
Alignment explanation
Indices: 41213943--41214011 Score: 61
Period size: 11 Copynumber: 6.4 Consensus size: 11
41213933 CAACAACAGC
41213943 AAAAAAAA-CA
1 AAAAAAAAGCA
*
41213953 CAAAAAAAGCA
1 AAAAAAAAGCA
*
41213964 AAAAAAAAGCG
1 AAAAAAAAGCA
*
41213975 CAAAAAAAG-A
1 AAAAAAAAGCA
* **
41213985 GTAAAAAGCGCA
1 -AAAAAAAAGCA
41213997 AAAAAAAAGCA
1 AAAAAAAAGCA
41214008 AAAA
1 AAAA
41214012 GTAAAAAAGC
Statistics
Matches: 45, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
10 7 0.16
11 37 0.82
12 1 0.02
ACGTcount: A:0.75, C:0.12, G:0.12, T:0.01
Consensus pattern (11 bp):
AAAAAAAAGCA
Found at i:41214031 original size:20 final size:20
Alignment explanation
Indices: 41213967--41214012 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
41213957 AAAAGCAAAA
41213967 AAAAAGCGCAAAAAAAGAGT
1 AAAAAGCGCAAAAAAAGAGT
* *
41213987 AAAAAGCGCAAAAAAAAAGC
1 AAAAAGCGCAAAAAAAGAGT
41214007 AAAAAG
1 AAAAAG
41214013 TAAAAAAGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.70, C:0.11, G:0.17, T:0.02
Consensus pattern (20 bp):
AAAAAGCGCAAAAAAAGAGT
Found at i:41214034 original size:29 final size:28
Alignment explanation
Indices: 41213979--41214032 Score: 92
Period size: 28 Copynumber: 1.9 Consensus size: 28
41213969 AAAGCGCAAA
41213979 AAAAGAGTAAAAAGCGCAAAAAAAAAGC
1 AAAAGAGTAAAAAGCGCAAAAAAAAAGC
41214007 AAAA-AGTAAAAAAGCGCAAAAAAAAA
1 AAAAGAGT-AAAAAGCGCAAAAAAAAA
41214033 AGTTGCCTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 3 0.12
28 22 0.88
ACGTcount: A:0.72, C:0.09, G:0.15, T:0.04
Consensus pattern (28 bp):
AAAAGAGTAAAAAGCGCAAAAAAAAAGC
Found at i:41217099 original size:31 final size:31
Alignment explanation
Indices: 41217063--41217157 Score: 154
Period size: 31 Copynumber: 3.1 Consensus size: 31
41217053 CTTAGATAAT
*
41217063 TTTAAAGAGTTTTATTAGGATTCAATTATTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
* *
41217094 TTTAAAGATTTTTATTAGGATTCAATTACTA
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
*
41217125 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
41217156 TT
1 TT
41217158 GTAATTTGCC
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 58 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:41217787 original size:50 final size:51
Alignment explanation
Indices: 41217610--41217795 Score: 180
Period size: 51 Copynumber: 3.7 Consensus size: 51
41217600 TTCCTATAAA
* * * * * * * *
41217610 CACGTGTGTAGTACTAAGTGCAGGCTACTACGGGTATC-GATAGATAATGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGAACCAGAAAGCT-TTGAT
* * * * *
41217661 CACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCAGAAGGCTTTGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGAACCAGAAAGCTTTGAT
* *
41217712 CACGTGCGTAGTACTATATGCAGGCTACTACGTGAACC-GAAAAG-TTTGAT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGAACCAG-AAAGCTTTGAT
* *
41217762 CACGTGTGTAGTTCTATGTGAAGGCTACTACGTG
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTG
41217796 TGTCAAATGA
Statistics
Matches: 113, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
50 36 0.32
51 73 0.65
52 4 0.04
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGCAGGCTACTACGTGAACCAGAAAGCTTTGAT
Found at i:41221456 original size:27 final size:28
Alignment explanation
Indices: 41221426--41221483 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
41221416 AATGCATCCA
* *
41221426 TTTT-AGAGTTCGCCACAAAGGCTATTC
1 TTTTCAGAGTTCACCACAAAAGCTATTC
** *
41221453 TTTTCATTGTTCACCACAAAAGTTATTC
1 TTTTCAGAGTTCACCACAAAAGCTATTC
41221481 TTT
1 TTT
41221484 ACTGTTGTGT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 4 0.16
28 21 0.84
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.41
Consensus pattern (28 bp):
TTTTCAGAGTTCACCACAAAAGCTATTC
Found at i:41231425 original size:3 final size:3
Alignment explanation
Indices: 41231417--41231470 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
41231407 TTCCTTTCAA
41231417 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
41231465 AAT AAT
1 AAT AAT
41231471 GTAAAGCATG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:41232280 original size:18 final size:19
Alignment explanation
Indices: 41232236--41232285 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
41232226 TACCTTTATT
41232236 ACTATTTTACAAATTAAATAC
1 ACTA-TTTA-AAATTAAATAC
*
41232257 ACTA-TTAAAATTGAAATAG
1 ACTATTTAAAATT-AAATAC
41232276 A-TATTTAAAA
1 ACTATTTAAAA
41232286 ATATAAACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 7 0.27
19 15 0.58
21 4 0.15
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.36
Consensus pattern (19 bp):
ACTATTTAAAATTAAATAC
Found at i:41236547 original size:23 final size:22
Alignment explanation
Indices: 41236521--41237083 Score: 396
Period size: 23 Copynumber: 25.2 Consensus size: 22
41236511 AAGTAAAATT
*
41236521 ATTAACTTAGTTTAGGGTTTTTA
1 ATTAA-TTAGGTTAGGGTTTTTA
* *
41236544 ATTAACTTAGTTTAGGGTTTTAA
1 ATTAA-TTAGGTTAGGGTTTTTA
* *
41236567 AGTTAA--GGGTAAGGGTTTTTA
1 A-TTAATTAGGTTAGGGTTTTTA
* *
41236588 AGTTAA--GGGTTTAAGGTTTTTA
1 A-TTAATTAGG-TTAGGGTTTTTA
***
41236610 AGTTAAGGGGGTTAGGG-TTTTA
1 A-TTAATTAGGTTAGGGTTTTTA
*
41236632 AGTTAA--GGGTTAGGGTTTTTA
1 A-TTAATTAGGTTAGGGTTTTTA
* **
41236653 AGTAACGA-GTTAGGGTTTTTA
1 ATTAATTAGGTTAGGGTTTTTA
*
41236674 ATTTAATTAGCTTAGGG-TTTTA
1 A-TTAATTAGGTTAGGGTTTTTA
* *
41236696 GGGTTAA--GGGTTAGGGTTTTTA
1 --ATTAATTAGGTTAGGGTTTTTA
41236718 ATTAATTTAGGTTAGGGTTTTTA
1 ATTAA-TTAGGTTAGGGTTTTTA
*
41236741 ATTTAATTAGCTTAGGG-TTTTA
1 A-TTAATTAGGTTAGGGTTTTTA
* *
41236763 GGGTTAA--GGGTTAGGGTTTTTA
1 --ATTAATTAGGTTAGGGTTTTTA
*
41236785 ATTAAATTAGGTTAGGGATTTTA
1 ATT-AATTAGGTTAGGGTTTTTA
41236808 ATTTAATTAGGTTAGGG-TTTTA
1 A-TTAATTAGGTTAGGGTTTTTA
* *
41236830 GGGTTAA--GGGTTAGGG-TTTTA
1 --ATTAATTAGGTTAGGGTTTTTA
41236851 ATTAAATTAGGTTAGGGTTTTTA
1 ATT-AATTAGGTTAGGGTTTTTA
41236874 ATTTAATTAGGTTAGGGTTTTTA
1 A-TTAATTAGGTTAGGGTTTTTA
41236897 ATTAAATTAGGTTAGGGTTTTTTTA
1 ATT-AATTAGGTTAGGG--TTTTTA
* * *
41236922 TTTAATAAGGTTAGAG-TTTTA
1 ATTAATTAGGTTAGGGTTTTTA
** *
41236943 GGGT-ATTAGGTT-GGATTTTTA
1 -ATTAATTAGGTTAGGGTTTTTA
41236964 ATTAAATTAGGTTAGGG-TTTTA
1 ATT-AATTAGGTTAGGGTTTTTA
***
41236986 ATTTAATTAGGTTTTAGTTTTTA
1 A-TTAATTAGGTTAGGGTTTTTA
41237009 ATTAAATTAGGTTAGGGTTTTTA
1 ATT-AATTAGGTTAGGGTTTTTA
*
41237032 ATTTAATTAGGTTAGAGTTTTTA
1 A-TTAATTAGGTTAGGGTTTTTA
*
41237055 ATTAAATTAGGTTAGGATTTTTA
1 ATT-AATTAGGTTAGGGTTTTTA
41237078 AGTTAA
1 A-TTAA
41237084 GAGTATTAAT
Statistics
Matches: 446, Mismatches: 50, Indels: 88
0.76 0.09 0.15
Matches are distributed among these distances:
19 2 0.00
20 22 0.05
21 86 0.19
22 95 0.21
23 203 0.46
24 30 0.07
25 8 0.02
ACGTcount: A:0.27, C:0.01, G:0.25, T:0.47
Consensus pattern (22 bp):
ATTAATTAGGTTAGGGTTTTTA
Found at i:41236583 original size:21 final size:21
Alignment explanation
Indices: 41236557--41236722 Score: 126
Period size: 21 Copynumber: 7.8 Consensus size: 21
41236547 AACTTAGTTT
*
41236557 AGGGTTTTAAAGTTAAGGGTA
1 AGGGTTTTTAAGTTAAGGGTA
41236578 AGGGTTTTTAAGTTAAGGGTTTA
1 AGGGTTTTTAAGTTAAGGG--TA
*
41236601 A-GGTTTTTAAGTTAAGGGGGTT
1 AGGGTTTTTAAGTTAA--GGGTA
*
41236623 AGGG-TTTTAAGTTAAGGGTT
1 AGGGTTTTTAAGTTAAGGGTA
* *
41236643 AGGGTTTTTAAG-TAACGAGTT
1 AGGGTTTTTAAGTTAA-GGGTA
* * * *
41236664 AGGGTTTTTAATTTAATTAGCTT
1 AGGGTTTTTAAGTTAA--GGGTA
* *
41236687 AGGG-TTTTAGGGTTAAGGGTT
1 AGGGTTTTTA-AGTTAAGGGTA
41236708 AGGGTTTTTAA-TTAA
1 AGGGTTTTTAAGTTAA
41236723 TTTAGGTTAG
Statistics
Matches: 121, Mismatches: 13, Indels: 23
0.77 0.08 0.15
Matches are distributed among these distances:
20 16 0.13
21 47 0.39
22 40 0.33
23 15 0.12
24 3 0.02
ACGTcount: A:0.27, C:0.01, G:0.31, T:0.42
Consensus pattern (21 bp):
AGGGTTTTTAAGTTAAGGGTA
Found at i:41236733 original size:44 final size:43
Alignment explanation
Indices: 41236532--41237083 Score: 284
Period size: 44 Copynumber: 12.4 Consensus size: 43
41236522 TTAACTTAGT
*
41236532 TTAGGGTTTTTAATTAACTTAGTTTAGGGTTTTAAAGTTAA-GGG
1 TTAGGGTTTTTAATTAA-TTAGGTTAGGGTTTT-AAGTTAATGGG
* * * *
41236576 TAAGGGTTTTTAAGTTAA--GGGTTTAAGGTTTTTAAGTTAAGGGGG
1 TTAGGGTTTTTAA-TTAATTAGG-TT-AGGGTTTTAAGTTAA-TGGG
* * *
41236621 TTAGGG-TTTTAAGTTAA--GGGTTAGGGTTTTTAAG-TAACGAG
1 TTAGGGTTTTTAA-TTAATTAGGTTAGGG-TTTTAAGTTAATGGG
* *
41236662 TTAGGGTTTTTAATTTAATTAGCTTAGGGTTTTAGGGTTAA-GGG
1 TTAGGGTTTTTAA-TTAATTAGGTTAGGGTTTTA-AGTTAATGGG
* * *
41236706 TTAGGGTTTTTAATTAATTTAGGTTAGGGTTTTTAATTTAATTAGC
1 TTAGGGTTTTTAATTAA-TTAGGTTAGGG-TTTTAAGTTAA-TGGG
* * *
41236752 TTAGGG-TTTTAGGGTTAA--GGGTTAGGGTTTTTAA-TTAAATTAGG
1 TTAGGGTTTTTA--ATTAATTAGGTTAGGG-TTTTAAGTT-AA-TGGG
* *
41236796 TTAGGGATTTTAATTTAATTAGGTTAGGGTTTTAGGGTTAA-GGG
1 TTAGGGTTTTTAA-TTAATTAGGTTAGGGTTTTA-AGTTAATGGG
* *
41236840 TTAGGG-TTTTAATTAAATTAGGTTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAATT-AATTAGGTTAGGG-TTTTAAGTTAA-TGGG
* * *
41236885 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTTTATTTAATAAGG
1 TTAGGGTTTTTAATT-AATTAGGTTAGGG--TTTTAAGTTAAT-GGG
* ** * *
41236932 TTAGAG-TTTTAGGGT-ATTAGGTT-GGATTTTTAA-TTAAATTAGG
1 TTAGGGTTTTTA-ATTAATTAGGTTAGG-GTTTTAAGTT-AA-TGGG
* *
41236975 TTAGGG-TTTTAATTTAATTAGGTTTTA-GTTTTTAA-TTAAATTAGG
1 TTAGGGTTTTTAA-TTAATTAGG--TTAGGGTTTTAAGTT-AA-TGGG
* *
41237020 TTAGGGTTTTTAATTTAATTAGGTTAGAGTTTTTAA-TTAAATTAGG
1 TTAGGGTTTTTAA-TTAATTAGGTTAG-GGTTTTAAGTT-AA-TGGG
*
41237066 TTAGGATTTTTAAGTTAA
1 TTAGGGTTTTTAA-TTAA
41237084 GAGTATTAAT
Statistics
Matches: 426, Mismatches: 39, Indels: 84
0.78 0.07 0.15
Matches are distributed among these distances:
41 8 0.02
42 21 0.05
43 73 0.17
44 126 0.30
45 74 0.17
46 98 0.23
47 26 0.06
ACGTcount: A:0.27, C:0.01, G:0.25, T:0.47
Consensus pattern (43 bp):
TTAGGGTTTTTAATTAATTAGGTTAGGGTTTTAAGTTAATGGG
Found at i:41236896 original size:67 final size:66
Alignment explanation
Indices: 41236521--41237083 Score: 504
Period size: 67 Copynumber: 8.4 Consensus size: 66
41236511 AAGTAAAATT
* * * *
41236521 ATTAACTTAGTTTAGGGTTTTTAA-TTAACTTAGTTTAGGGTTTTAAAGTTAAGGGTAAGGGTTT
1 ATTAAATTAGGTTAGGGTTTTTAATTTAA-TTAGGTTAGGGTTTT-AAGTTAAGGGTTAGGGTTT
41236585 TTA
64 TTA
* * * ***
41236588 AGTT-AA--GGGTTTAAGGTTTTTAAGTTAAGGGGGTTAGGGTTTTAAGTTAAGGGTTAGGGTTT
1 A-TTAAATTAGG-TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTAAGTTAAGGGTTAGGGTTT
41236650 TTA
64 TTA
* ** * *
41236653 AGT-AACGA-GTTAGGGTTTTTAATTTAATTAGCTTAGGGTTTTAGGGTTAAGGGTTAGGGTTTT
1 ATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTA-AGTTAAGGGTTAGGGTTTT
41236716 TA
65 TA
* * *
41236718 ATTAATTTAGGTTAGGGTTTTTAATTTAATTAGCTTAGGGTTTTAGGGTTAAGGGTTAGGGTTTT
1 ATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTA-AGTTAAGGGTTAGGGTTTT
41236783 TA
65 TA
* *
41236785 ATTAAATTAGGTTAGGGATTTTAATTTAATTAGGTTAGGGTTTTAGGGTTAAGGGTTAGGG-TTT
1 ATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTA-AGTTAAGGGTTAGGGTTTT
41236849 TA
65 TA
*
41236851 ATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAA-TTAAATTAGGTTAGGGT
1 ATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGG-TTTTAAGTT-AA--GGGTTAGGG-
*
41236915 TTTTTT
61 TTTTTA
* * * *** * *
41236921 ATTTAATAAGGTTAGAG-TTTTAGGGT-ATTAGGTT-GGATTTTTAA-TTAAATTAGGTTAGGG-
1 ATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGG-GTTTTAAGTT-AA--GGGTTAGGGT
41236981 TTTTA
62 TTTTA
* *** * * * *
41236986 ATTTAATTAGGTTTTAGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGAGTT
1 ATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGG-TTTTAAGTTAA--GGGTTAGGGTT
41237051 TTTA
63 TTTA
* *
41237055 ATTAAATTAGGTTAGGATTTTTAAGTTAA
1 ATTAAATTAGGTTAGGGTTTTTAATTTAA
41237084 GAGTATTAAT
Statistics
Matches: 422, Mismatches: 53, Indels: 40
0.82 0.10 0.08
Matches are distributed among these distances:
64 31 0.07
65 66 0.16
66 76 0.18
67 158 0.37
68 38 0.09
69 35 0.08
70 18 0.04
ACGTcount: A:0.27, C:0.01, G:0.25, T:0.47
Consensus pattern (66 bp):
ATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTAAGTTAAGGGTTAGGGTTTTT
A
Found at i:41236901 original size:112 final size:111
Alignment explanation
Indices: 41236726--41237052 Score: 446
Period size: 112 Copynumber: 2.9 Consensus size: 111
41236716 TAATTAATTT
* * ** *
41236726 AGGTTAGGGTTTTTAATTTAATTAGCTTAGGGTTTTAGGGTTAA--GGGTTAGGGTTTTTAATTA
1 AGGTTAGGG-TTTTAATTAAATTAGGTTAGGGTTTTA-ATTTAATTAGGTTAGGGTTTTTAATTA
* *
41236789 AATTAGGTTAGGGATTTTAATTTAATTAGGTTAGGGTTTTAGGGT-TA
64 AATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGAGTTTTAGGGTATA
41236836 AGGGTTAGGGTTTTAATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTA
1 A-GGTTAGGGTTTTAATTAAATTAGGTTAGGG-TTTTAATTTAATTAGGTTAGGGTTTTTAATTA
* * *
41236901 AATTAGGTTAGGGTTTTTTTATTTAATAAGGTTAGAGTTTTAGGGTATT
64 AATTAGGTTAGGG-TTTTTAATTTAATTAGGTTAGAGTTTTAGGGTATA
* ***
41236950 AGGTT-GGATTTTTAATTAAATTAGGTTAGGGTTTTAATTTAATTAGGTTTTAGTTTTTAATTAA
1 AGGTTAGG-GTTTTAATTAAATTAGGTTAGGGTTTTAATTTAATTAGGTTAGGGTTTTTAATTAA
41237014 ATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGAGTTTT
65 ATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGAGTTTT
41237053 TAATTAAATT
Statistics
Matches: 194, Mismatches: 16, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
110 25 0.13
111 38 0.20
112 75 0.39
113 54 0.28
114 2 0.01
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.48
Consensus pattern (111 bp):
AGGTTAGGGTTTTAATTAAATTAGGTTAGGGTTTTAATTTAATTAGGTTAGGGTTTTTAATTAAA
TTAGGTTAGGGTTTTTAATTTAATTAGGTTAGAGTTTTAGGGTATA
Found at i:41237164 original size:25 final size:25
Alignment explanation
Indices: 41237135--41237389 Score: 178
Period size: 25 Copynumber: 10.9 Consensus size: 25
41237125 ATTCAAAAAT
41237135 TTCTATTTTATTACATCAAATAAAC
1 TTCTATTTTATTACATCAAATAAAC
41237160 TTCTATTTTATTACATCAAAT-AA-
1 TTCTATTTTATTACATCAAATAAAC
** * * *
41237183 TATC-A--ACATAAC-T-AAAAAAAT
1 T-TCTATTTTATTACATCAAATAAAC
41237204 TTCTATTTTATTACATCAAATAAAC
1 TTCTATTTTATTACATCAAATAAAC
*
41237229 TTCTATTTTATCACATCAAAT-AA-
1 TTCTATTTTATTACATCAAATAAAC
* * * *
41237252 TATC-A---AAATAGC-T-AAAAAAAA
1 T-TCTATTTTATTA-CATCAAATAAAC
41237273 TTCTATTTTATTACATCAAATAAAC
1 TTCTATTTTATTACATCAAATAAAC
41237298 TTCTATTTTATTACATCAAAT-AA-
1 TTCTATTTTATTACATCAAATAAAC
** * *
41237321 TATC-A--AAATAAC-T-AAA-AACAA
1 T-TCTATTTTATTACATCAAATAA-AC
41237342 TTCTATTTTATTACATCAAATAAAC
1 TTCTATTTTATTACATCAAATAAAC
41237367 TTCTATTTTATTACATCAAATAA
1 TTCTATTTTATTACATCAAATAA
41237390 TATCAAAATA
Statistics
Matches: 177, Mismatches: 25, Indels: 56
0.69 0.10 0.22
Matches are distributed among these distances:
19 10 0.06
20 16 0.09
21 15 0.08
23 15 0.08
24 18 0.10
25 101 0.57
26 2 0.01
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.39
Consensus pattern (25 bp):
TTCTATTTTATTACATCAAATAAAC
Found at i:41237217 original size:69 final size:69
Alignment explanation
Indices: 41237108--41237399 Score: 500
Period size: 69 Copynumber: 4.3 Consensus size: 69
41237098 AGTAGAATTC
**
41237108 TCAAATAATATCAAAAT-A-TTCAAAAATTTCTATTTTATTACATCAAATAAACTTCTATTTTAT
1 TCAAATAATATCAAAATAACTAAAAAAATTTCTATTTTATTACATCAAATAAACTTCTATTTTAT
41237171 TACA
66 TACA
*
41237175 TCAAATAATATCAACATAACTAAAAAAATTTCTATTTTATTACATCAAATAAACTTCTATTTTAT
1 TCAAATAATATCAAAATAACTAAAAAAATTTCTATTTTATTACATCAAATAAACTTCTATTTTAT
*
41237240 CACA
66 TACA
* *
41237244 TCAAATAATATCAAAATAGCTAAAAAAAATTCTATTTTATTACATCAAATAAACTTCTATTTTAT
1 TCAAATAATATCAAAATAACTAAAAAAATTTCTATTTTATTACATCAAATAAACTTCTATTTTAT
41237309 TACA
66 TACA
41237313 TCAAATAATATCAAAATAACTAAAAACAA-TTCTATTTTATTACATCAAATAAACTTCTATTTTA
1 TCAAATAATATCAAAATAACTAAAAA-AATTTCTATTTTATTACATCAAATAAACTTCTATTTTA
41237377 TTACA
65 TTACA
41237382 TCAAATAATATCAAAATA
1 TCAAATAATATCAAAATA
41237400 TTCAAAATAT
Statistics
Matches: 213, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
67 16 0.08
68 1 0.00
69 194 0.91
70 2 0.01
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (69 bp):
TCAAATAATATCAAAATAACTAAAAAAATTTCTATTTTATTACATCAAATAAACTTCTATTTTAT
TACA
Found at i:41238499 original size:7 final size:7
Alignment explanation
Indices: 41238489--41238514 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
41238479 TTATATACAT
41238489 AATACTA
1 AATACTA
41238496 AATACTA
1 AATACTA
41238503 AATACTA
1 AATACTA
41238510 AATAC
1 AATAC
41238515 CAGTCGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:41239721 original size:11 final size:11
Alignment explanation
Indices: 41239707--41239746 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
41239697 GAATTTTGGA
41239707 AGGAAATTAAG
1 AGGAAATTAAG
41239718 AGGAAATTAAG
1 AGGAAATTAAG
*
41239729 AGGAAATTGAG
1 AGGAAATTAAG
*
41239740 AGAAAAT
1 AGGAAAT
41239747 ATGAGAAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.28, T:0.17
Consensus pattern (11 bp):
AGGAAATTAAG
Found at i:41241134 original size:26 final size:25
Alignment explanation
Indices: 41241092--41241436 Score: 158
Period size: 25 Copynumber: 13.6 Consensus size: 25
41241082 TAAAAAATAA
* * *
41241092 TTTAAAGTATATAATATA-AAAAGG
1 TTTAAAATAAATAATATATAAAAAG
*
41241116 TTTAAAATAAATAATATATGAAAACCAA
1 TTTAAAATAAATAATATAT-AAAA--AG
* *
41241144 TTTAAAATAAATAATATACAAAATGG
1 TTTAAAATAAATAATATATAAAA-AG
* **
41241170 TTCAAAATAAACCATATGA-AAAAA-
1 TTTAAAATAAATAATAT-ATAAAAAG
* ** *
41241194 CTTATCATAAATAAAATATAAAATAG
1 TTTAAAATAAATAATATATAAAA-AG
**
41241220 -TTCGAAT--AT-ATATATAAAGCAA-
1 TTTAAAATAAATAATATATAAA--AAG
*
41241242 TTTAAAATAAATAATATATATAATAG
1 TTTAAAATAAATAATATATA-AAAAG
*
41241268 TTTAAAATAATATACA-ATA-AAACAG
1 TTTAAAATAA-ATA-ATATATAAAAAG
* * ** *
41241293 TTTGAAATGAATACCATATAAAAAA
1 TTTAAAATAAATAATATATAAAAAG
* *
41241318 TTTAACATTAATAA-AGTATAAAATAG
1 TTTAAAATAAATAATA-TATAAAA-AG
*
41241344 TTTAAAAT-AATAATATATGAAAAAAAA
1 TTTAAAATAAATAATATAT---AAAAAG
* * *
41241371 CTTAAAATAAGTAATA-ATAAAACAA
1 TTTAAAATAAATAATATATAAAA-AG
* *
41241396 TTTAAAATAAGTAATATATGAAAAGAT
1 TTTAAAATAAATAATATAT-AAAA-AG
41241423 TTTAAAATAAATAA
1 TTTAAAATAAATAA
41241437 ATAAACAACA
Statistics
Matches: 246, Mismatches: 45, Indels: 57
0.71 0.13 0.16
Matches are distributed among these distances:
22 8 0.03
23 9 0.04
24 42 0.17
25 66 0.27
26 51 0.21
27 41 0.17
28 29 0.12
ACGTcount: A:0.59, C:0.05, G:0.06, T:0.30
Consensus pattern (25 bp):
TTTAAAATAAATAATATATAAAAAG
Found at i:41241146 original size:52 final size:54
Alignment explanation
Indices: 41241072--41241180 Score: 141
Period size: 52 Copynumber: 2.1 Consensus size: 54
41241062 AAACGAAACA
* * * * *
41241072 AAATAATATGTAAAAAATAATTTAAAGTATATAATATA-AAAA-GGTTTAAAAT
1 AAATAATATATAAAAAACAATTTAAAATAAATAATATACAAAATGGTTCAAAAT
* *
41241124 AAATAATATATGAAAACCAATTTAAAATAAATAATATACAAAATGGTTCAAAAT
1 AAATAATATATAAAAAACAATTTAAAATAAATAATATACAAAATGGTTCAAAAT
41241178 AAA
1 AAA
41241181 CCATATGAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
52 32 0.67
53 4 0.08
54 12 0.25
ACGTcount: A:0.61, C:0.04, G:0.06, T:0.29
Consensus pattern (54 bp):
AAATAATATATAAAAAACAATTTAAAATAAATAATATACAAAATGGTTCAAAAT
Found at i:41241261 original size:48 final size:50
Alignment explanation
Indices: 41241131--41241277 Score: 138
Period size: 48 Copynumber: 2.9 Consensus size: 50
41241121 AATAAATAAT
* *
41241131 ATATGAAAACCAATTTAAAATAAATAATATACAAAATGGTTCAAAATAAACC
1 ATATG-AAA-CAATTTAAAATAAATAATATATAAAATAGTTCAAAATAAACC
* * ** * * * *
41241183 ATATGAAAAAACTTATCATAAATAAAATATAAAATAGTTC-GAATATA-T
1 ATATGAAACAATTTAAAATAAATAATATATAAAATAGTTCAAAATAAACC
* *
41241231 ATAT-AAAGCAATTTAAAATAAATAATATATATAATAGTTTAAAATAA
1 ATATGAAA-CAATTTAAAATAAATAATATATAAAATAGTTCAAAATAA
41241278 TATACAATAA
Statistics
Matches: 74, Mismatches: 19, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
47 3 0.04
48 29 0.39
49 9 0.12
50 25 0.34
51 3 0.04
52 5 0.07
ACGTcount: A:0.58, C:0.07, G:0.05, T:0.30
Consensus pattern (50 bp):
ATATGAAACAATTTAAAATAAATAATATATAAAATAGTTCAAAATAAACC
Found at i:41241427 original size:27 final size:27
Alignment explanation
Indices: 41241344--41241432 Score: 112
Period size: 27 Copynumber: 3.4 Consensus size: 27
41241334 TATAAAATAG
41241344 TTTAAAATAA-TAATATATGAAAAAAAA
1 TTTAAAATAAGTAATATATG-AAAAAAA
* *
41241371 CTTAAAATAAGTAATA-AT-AAAACAA
1 TTTAAAATAAGTAATATATGAAAAAAA
* *
41241396 TTTAAAATAAGTAATATATGAAAAGAT
1 TTTAAAATAAGTAATATATGAAAAAAA
41241423 TTTAAAATAA
1 TTTAAAATAA
41241433 ATAAATAAAC
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
25 21 0.39
26 2 0.04
27 26 0.48
28 5 0.09
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (27 bp):
TTTAAAATAAGTAATATATGAAAAAAA
Found at i:41241451 original size:53 final size:52
Alignment explanation
Indices: 41241335--41241436 Score: 134
Period size: 52 Copynumber: 2.0 Consensus size: 52
41241325 TTAATAAAGT
* * *
41241335 ATAAAATAGTTTAAAATAATAATATATGAAAAAAAACTTAAAATAAGTAATA
1 ATAAAACAATTTAAAATAATAATATATGAAAAAAAACTTAAAATAAATAATA
* **
41241387 ATAAAACAATTTAAAATAAGTAATATATG-AAAAGATTTTAAAATAAATAA
1 ATAAAACAATTTAAAATAA-TAATATATGAAAAAAAACTTAAAATAAATAA
41241437 ATAAACAACA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
52 34 0.79
53 9 0.21
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (52 bp):
ATAAAACAATTTAAAATAATAATATATGAAAAAAAACTTAAAATAAATAATA
Found at i:41242846 original size:26 final size:25
Alignment explanation
Indices: 41242804--41243147 Score: 172
Period size: 26 Copynumber: 13.6 Consensus size: 25
41242794 TAAAAAATAA
* *
41242804 TTTAAAGTAAATAATATA-AAAAGG
1 TTTAAAATAAATAATATATAAAAAG
*
41242828 TTTAAAATAAATAATATATGAAAAAA
1 TTTAAAATAAATAATATAT-AAAAAG
* * *
41242854 ATTAAAATAAATAATATACAAAATGG
1 TTTAAAATAAATAATATATAAAA-AG
* **
41242880 TTCAAAATAAACCATATGA-AAAAA-
1 TTTAAAATAAATAATAT-ATAAAAAG
* ** *
41242904 CTTATCATAAATAAAATATAAAATAG
1 TTTAAAATAAATAATATATAAAA-AG
*
41242930 -TT-CAA-AAAT-ATATATAAAGCAA-
1 TTTAAAATAAATAATATATAAA--AAG
*
41242952 TTTAAAATAAATAATATATATAATAG
1 TTTAAAATAAATAATATATA-AAAAG
* *
41242978 TTTTAAATAATATACA-ATA-AAACAG
1 TTTAAAATAA-ATA-ATATATAAAAAG
* * ** *
41243003 TTTGAAATGAATACCATATAAAACAA
1 TTTAAAATAAATAATATATAAAA-AG
* * *
41243029 TTTAAAATTAATAATGTATAAAATAA
1 TTTAAAATAAATAATATATAAAA-AG
*
41243055 TTTAAAAT-AATAATATATGAAAAAAAA
1 TTTAAAATAAATAATATAT---AAAAAG
* *
41243082 CTTAAAATAAGTAATA-ATAAAATAG
1 TTTAAAATAAATAATATATAAAA-AG
* * *
41243107 TTAAAAATAAGTAATATATGAAAAGAT
1 TTTAAAATAAATAATATAT-AAAA-AG
41243134 TTTAAAATAAATAA
1 TTTAAAATAAATAA
41243148 ATAAACAATA
Statistics
Matches: 246, Mismatches: 47, Indels: 51
0.72 0.14 0.15
Matches are distributed among these distances:
22 8 0.03
23 8 0.03
24 45 0.18
25 51 0.21
26 86 0.35
27 37 0.15
28 11 0.04
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (25 bp):
TTTAAAATAAATAATATATAAAAAG
Found at i:41242852 original size:52 final size:52
Alignment explanation
Indices: 41242784--41242969 Score: 154
Period size: 50 Copynumber: 3.7 Consensus size: 52
41242774 AAACGAAACA
* * *
41242784 AAATAATATGTAAAAAATAATTTAAAGTAAATAATATA-AAAA-GGTTTAAAAT
1 AAATAATATATAAAAAA-AA-TTAAAATAAATAATATACAAAATGGTTCAAAAT
*
41242836 AAATAATATATGAAAAAAATTAAAATAAATAATATACAAAATGGTTCAAAAT
1 AAATAATATATAAAAAAAATTAAAATAAATAATATACAAAATGGTTCAAAAT
** * * ** * * *
41242888 -AA-ACCATATGAAAAAACTTATCATAAATAAAATATAAAATAGTTC--AA-
1 AAATAATATATAAAAAAAATTAAAATAAATAATATACAAAATGGTTCAAAAT
** *
41242935 AAAT-ATATATAAAGCAATTTAAAATAAATAATATA
1 AAATAATATATAAAAAAAATTAAAATAAATAATATA
41242970 TATAATAGTT
Statistics
Matches: 109, Mismatches: 21, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
48 26 0.24
50 51 0.47
51 8 0.07
52 24 0.22
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.28
Consensus pattern (52 bp):
AAATAATATATAAAAAAAATTAAAATAAATAATATACAAAATGGTTCAAAAT
Found at i:41245162 original size:18 final size:19
Alignment explanation
Indices: 41245123--41245159 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
41245113 TAGATATATG
*
41245123 TTATTTTTAAAATTAAAAA
1 TTATTTTCAAAATTAAAAA
41245142 TTATTTTCAAAATTAAAA
1 TTATTTTCAAAATTAAAA
41245160 TTAAAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (19 bp):
TTATTTTCAAAATTAAAAA
Found at i:41245867 original size:13 final size:13
Alignment explanation
Indices: 41245847--41245882 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
41245837 CAAATAAATT
41245847 GAAGAAAAA-AAA
1 GAAGAAAAAGAAA
41245859 GAGAGAAAAAGAAA
1 GA-AGAAAAAGAAA
41245873 GAAGAAAAAG
1 GAAGAAAAAG
41245883 GCGAGAAGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 2 0.09
13 15 0.68
14 5 0.23
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (13 bp):
GAAGAAAAAGAAA
Found at i:41249275 original size:12 final size:12
Alignment explanation
Indices: 41249258--41249282 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41249248 TTGGGAATTC
41249258 TTCCAAAAGAAA
1 TTCCAAAAGAAA
41249270 TTCCAAAAGAAA
1 TTCCAAAAGAAA
41249282 T
1 T
41249283 ATGTTGGCGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.16, G:0.08, T:0.20
Consensus pattern (12 bp):
TTCCAAAAGAAA
Found at i:41257428 original size:41 final size:42
Alignment explanation
Indices: 41257382--41257469 Score: 106
Period size: 41 Copynumber: 2.1 Consensus size: 42
41257372 TCCACAAAAA
* * *
41257382 ATTGTGGAATATGTTGTTGTTCAATATCTGGTTCAATGATCT
1 ATTGTGGAATATATTATTATTCAATATCTGGTTCAATGATCT
* * * *
41257424 -TTGTGGAATCTATTATTATTCAATCTCTGGTTTAGTGATCT
1 ATTGTGGAATATATTATTATTCAATATCTGGTTCAATGATCT
41257465 ATTGT
1 ATTGT
41257470 TATTCTATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 34 0.89
42 4 0.11
ACGTcount: A:0.23, C:0.10, G:0.19, T:0.48
Consensus pattern (42 bp):
ATTGTGGAATATATTATTATTCAATATCTGGTTCAATGATCT
Found at i:41263967 original size:20 final size:20
Alignment explanation
Indices: 41263942--41263980 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
41263932 TACTTTATTC
41263942 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
41263962 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
41263981 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:41266511 original size:48 final size:48
Alignment explanation
Indices: 41266440--41266535 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 48
41266430 ACATGAGTAA
*
41266440 GCTTTAATAGAGCTTAGTAAGTTCAACAGTTGAATCAATAAAACTTAC
1 GCTTTAATAGAGCCTAGTAAGTTCAACAGTTGAATCAATAAAACTTAC
* *
41266488 GCTTTAATAGAGCCTAGTAAGTTCAACGGTTGAATTAATAAAACTTAC
1 GCTTTAATAGAGCCTAGTAAGTTCAACAGTTGAATCAATAAAACTTAC
41266536 CATATAAACA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (48 bp):
GCTTTAATAGAGCCTAGTAAGTTCAACAGTTGAATCAATAAAACTTAC
Found at i:41269049 original size:50 final size:50
Alignment explanation
Indices: 41268985--41269117 Score: 185
Period size: 50 Copynumber: 2.7 Consensus size: 50
41268975 CACTGTCATA
** * * *
41268985 TCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCTTG
1 TCCCAGATATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATG
** *
41269035 TCCCAGATATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATG
1 TCCCAGATATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATG
*
41269085 TCCCAGACATGGTCTTACATGGGACCTCTCATA
1 TCCCAGATATGGTCTTACATGGGACCTCTCATA
41269118 ACCTCAATGA
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 71 1.00
ACGTcount: A:0.20, C:0.29, G:0.23, T:0.28
Consensus pattern (50 bp):
TCCCAGATATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATG
Found at i:41276630 original size:50 final size:50
Alignment explanation
Indices: 41276510--41276696 Score: 130
Period size: 50 Copynumber: 3.8 Consensus size: 50
41276500 CATGCCAAAG
* * * *
41276510 CCATGTCCCAGACATGGTCTTACATGGGATGTT-TCTTGTACA--GCCACTA
1 CCATGTCCCAAACATGGTCTTACATGGGA-GTTCTCATAT-CAGTGCCCCTA
* * * * * *
41276559 TCATATCCCAGATATGATCTTACATGAGAGTTCTCATATCAGTGCCCCTA
1 CCATGTCCCAAACATGGTCTTACATGGGAGTTCTCATATCAGTGCCCCTA
** ** * * **
41276609 CCATGTCCCAAACATGGTCTTACGGGGGACCTCTCATCTCGGTG-CCAAA
1 CCATGTCCCAAACATGGTCTTACATGGGAGTTCTCATATCAGTGCCCCTA
* **
41276658 GCAATGTCCCAAACATGGTCTTACATGGGACCTCTCATA
1 -CCATGTCCCAAACATGGTCTTACATGGGAGTTCTCATA
41276697 ACCTCAATGA
Statistics
Matches: 108, Mismatches: 26, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
48 5 0.05
49 31 0.29
50 72 0.67
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (50 bp):
CCATGTCCCAAACATGGTCTTACATGGGAGTTCTCATATCAGTGCCCCTA
Found at i:41276721 original size:56 final size:50
Alignment explanation
Indices: 41276609--41276748 Score: 145
Period size: 56 Copynumber: 2.7 Consensus size: 50
41276599 AGTGCCCCTA
** *
41276609 CCATGTCCCAAACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAAAG
1 CCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGATGCCAAAG
* **
41276659 CAATGTCCCAAACATGGTCTTACATGGGACCTCTCATAACCTCAATGATGCCAATT
1 CCATGTCCCAAACATGGTCTTACATGGGACCTCTCAT---CTC---GATGCCAAAG
** *
41276715 CCATGTCCCTGACATGGTCTTACATGGGATCTCT
1 CCATGTCCCAAACATGGTCTTACATGGGACCTCT
41276749 TTACTCAAAT
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
50 34 0.46
53 3 0.04
56 37 0.50
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.26
Consensus pattern (50 bp):
CCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGATGCCAAAG
Found at i:41283521 original size:30 final size:30
Alignment explanation
Indices: 41283485--41283551 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
41283475 CTATTATCTT
41283485 CATTTTTATTTTATTTCCTTCATCTTCCAC
1 CATTTTTATTTTATTTCCTTCATCTTCCAC
41283515 CATTTTTATTTTATTTCCTTCATCTTCCAC
1 CATTTTTATTTTATTTCCTTCATCTTCCAC
41283545 CATTTTT
1 CATTTTT
41283552 CATCACTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.16, C:0.25, G:0.00, T:0.58
Consensus pattern (30 bp):
CATTTTTATTTTATTTCCTTCATCTTCCAC
Found at i:41284180 original size:18 final size:20
Alignment explanation
Indices: 41284159--41284202 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 20
41284149 TGTGTTTTAA
41284159 ATTTTATAG-T-TTAATTTT
1 ATTTTATAGTTATTAATTTT
*
41284177 ATTTTGTAGTTATTAATTTT
1 ATTTTATAGTTATTAATTTT
41284197 -TTTTAT
1 ATTTTAT
41284203 CTTTTAAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 8 0.36
19 6 0.27
20 8 0.36
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (20 bp):
ATTTTATAGTTATTAATTTT
Found at i:41298317 original size:54 final size:54
Alignment explanation
Indices: 41298258--41298370 Score: 147
Period size: 54 Copynumber: 2.1 Consensus size: 54
41298248 TGTCCTAAAT
* * *
41298258 CGTGTAACTCACTAACTTGGGTCACAC-AGTCGTGTCGTAGGTCGTGTGCCAGAC
1 CGTGTAACTCACTAACTTGGGTCACACGA-CCGTATCGCAGGTCGTGTGCCAGAC
* * * *
41298312 CGTGTAACTCTCTGACTTGTGTCACACGACCGTATCGCAGGTCGTGTGCTAGAC
1 CGTGTAACTCACTAACTTGGGTCACACGACCGTATCGCAGGTCGTGTGCCAGAC
41298366 CGTGT
1 CGTGT
41298371 CGCAGGCCGT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 50 0.98
55 1 0.02
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (54 bp):
CGTGTAACTCACTAACTTGGGTCACACGACCGTATCGCAGGTCGTGTGCCAGAC
Found at i:41298393 original size:24 final size:24
Alignment explanation
Indices: 41298339--41298394 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
41298329 TGTGTCACAC
* *
41298339 GACCGTATCGCAGGTCGTGTGCTA
1 GACCGTGTCGCAGGCCGTGTGCTA
41298363 GACCGTGTCGCAGGCCGTGTGCTA
1 GACCGTGTCGCAGGCCGTGTGCTA
*
41298387 GATCGTGT
1 GACCGTGT
41298395 AACTCACTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.14, C:0.25, G:0.36, T:0.25
Consensus pattern (24 bp):
GACCGTGTCGCAGGCCGTGTGCTA
Found at i:41305246 original size:2 final size:2
Alignment explanation
Indices: 41305239--41305279 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
41305229 CAAAGATGAC
41305239 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
41305280 TTATTTGTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:41308128 original size:173 final size:172
Alignment explanation
Indices: 41307838--41308169 Score: 454
Period size: 173 Copynumber: 1.9 Consensus size: 172
41307828 TAAAGCAAGG
* * * *
41307838 TATGATAAGATTATGCAAAAAAAAAATTATATTAGGAGTTATTTAATCATGAGTTTTTTTATCAT
1 TATGATAAGATTATGCAAAAAAAAAATTATATTAGGAGTCATTCAATCATGAATTATTTTATCAT
* * * *
41307903 TAAATTATGAAAAATTACAATATGATTATTTAACTATTCAATTTTGTATTATTCTAGCCACGT-A
66 TAAATTATGAAAAATTACAATATAATCATTTAACTATTCAAATTTATATTATTCTAGCCAC-TAA
41307967 ACTATATTAAATTTTAGAGTGCTTCCATTTCTATGTAACATGC
130 ACTATATTAAATTTTAGAGTGCTTCCATTTCTATGTAACATGC
*
41308010 TATGATAAGATTATG-AAAAAAAACTAGATTATATTAGTAGTCATTCAATCAT-AATTATTTTAT
1 TATGATAAGATTATGCAAAAAAAA--A-ATTATATTAGGAGTCATTCAATCATGAATTATTTTAT
* * * * *
41308073 CATTCAATTATGAAAATTTACAATATAATCATTTAATTATTCAAATTTATATTATTCTGGTCACT
63 CATTAAATTATGAAAAATTACAATATAATCATTTAACTATTCAAATTTATATTATTCTAGCCACT
* * *
41308138 AAACTATATTAGATTTTAGAGTGTTTTCATTT
128 AAACTATATTAAATTTTAGAGTGCTTCCATTT
41308170 TACGTTAGTC
Statistics
Matches: 139, Mismatches: 17, Indels: 7
0.85 0.10 0.04
Matches are distributed among these distances:
171 8 0.06
172 16 0.12
173 93 0.67
174 22 0.16
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (172 bp):
TATGATAAGATTATGCAAAAAAAAAATTATATTAGGAGTCATTCAATCATGAATTATTTTATCAT
TAAATTATGAAAAATTACAATATAATCATTTAACTATTCAAATTTATATTATTCTAGCCACTAAA
CTATATTAAATTTTAGAGTGCTTCCATTTCTATGTAACATGC
Done.