Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 8 of 226
Found at i:3369537 original size:11 final size:11
Alignment explanation
Indices: 3369521--3369555 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
3369511 AATGAATAAA
3369521 ATATTTTTTTT
1 ATATTTTTTTT
*
3369532 ATATTTTTTTA
1 ATATTTTTTTT
3369543 ATAATTTTTTTT
1 AT-ATTTTTTTT
3369555 A
1 A
3369556 AAAAAATACG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 12 0.57
12 9 0.43
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
ATATTTTTTTT
Found at i:3369551 original size:13 final size:12
Alignment explanation
Indices: 3369520--3369556 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
3369510 GAATGAATAA
3369520 AATATTTTTTTT
1 AATATTTTTTTT
3369532 -ATA-TTTTTTT
1 AATATTTTTTTT
3369542 AATAATTTTTTTT
1 AAT-ATTTTTTTT
3369555 AA
1 AA
3369557 AAAAATACGG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
10 7 0.32
11 5 0.23
12 1 0.05
13 9 0.41
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
AATATTTTTTTT
Found at i:3369647 original size:27 final size:27
Alignment explanation
Indices: 3369617--3369678 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
3369607 CCTATCAGGT
3369617 AGGCGCCAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
*
3369644 AGGCGCCAATGAAGGTGCCTTATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
3369671 AGGCGCCA
1 AGGCGCCA
3369679 TTACTAGACC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.29, C:0.23, G:0.34, T:0.15
Consensus pattern (27 bp):
AGGCGCCAATGAAGGTGCCTCATAGAG
Found at i:3371020 original size:26 final size:26
Alignment explanation
Indices: 3370984--3371035 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
3370974 GTAAGAATCT
3370984 TCACAGTTTATTCCAACATATACATA
1 TCACAGTTTATTCCAACATATACATA
*
3371010 TCACAGTTTATTTCAACATATACATA
1 TCACAGTTTATTCCAACATATACATA
3371036 GAGAACCTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.37
Consensus pattern (26 bp):
TCACAGTTTATTCCAACATATACATA
Found at i:3372832 original size:42 final size:42
Alignment explanation
Indices: 3372729--3372833 Score: 138
Period size: 42 Copynumber: 2.5 Consensus size: 42
3372719 TTTTACTTTC
* *
3372729 CGTTTAGCTCTCACGAGCTTCTGTTTAACCCTTATGGGTTTT
1 CGTTCAGCTCTTACGAGCTTCTGTTTAACCCTTATGGGTTTT
* * *** *
3372771 CATTCAACTCTTTTAAGCTTTTGTTTAACCCTTATGGGTTTT
1 CGTTCAGCTCTTACGAGCTTCTGTTTAACCCTTATGGGTTTT
3372813 CGTTCAGCTCTTACGAGCTTC
1 CGTTCAGCTCTTACGAGCTTC
3372834 CATAAGGGTT
Statistics
Matches: 49, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.44
Consensus pattern (42 bp):
CGTTCAGCTCTTACGAGCTTCTGTTTAACCCTTATGGGTTTT
Found at i:3377183 original size:2 final size:2
Alignment explanation
Indices: 3377178--3377210 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3377168 CACCAAATCC
*
3377178 TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3377211 TAGTATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3378100 original size:42 final size:43
Alignment explanation
Indices: 3378053--3378153 Score: 134
Period size: 43 Copynumber: 2.4 Consensus size: 43
3378043 GCTCCCGGTA
*
3378053 TCGCACACTTAGTGCCC-GTTATTCAATATC-TCCATTTTAATT
1 TCGCACACTTAGTGCCCTGTTATTCAACATCAT-CATTTTAATT
* * *
3378095 TCGCACACTTAGTGCCCTTTTATTCAACCTCATCATTTTAGTT
1 TCGCACACTTAGTGCCCTGTTATTCAACATCATCATTTTAATT
*
3378138 CCGCACACTTAGTGCC
1 TCGCACACTTAGTGCC
3378154 GTTTATATAA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
42 17 0.33
43 34 0.65
44 1 0.02
ACGTcount: A:0.22, C:0.30, G:0.11, T:0.38
Consensus pattern (43 bp):
TCGCACACTTAGTGCCCTGTTATTCAACATCATCATTTTAATT
Found at i:3380818 original size:67 final size:67
Alignment explanation
Indices: 3380696--3380827 Score: 228
Period size: 67 Copynumber: 2.0 Consensus size: 67
3380686 GTTTATATTA
3380696 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATAAGGTACGCAGGAGTGTGCTCTCT
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATAAGGTACGCAGGAGTGTGCTCTCT
3380761 TG
66 TG
* * * *
3380763 CAGGGGATTTAGCCTGGACTGGTAATCCCGTTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCT
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATAAGGTACGCAGGAGTGTGCTCTCT
3380828 GAATTGGAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.27
Consensus pattern (67 bp):
CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATAAGGTACGCAGGAGTGTGCTCTCT
TG
Found at i:3382956 original size:34 final size:35
Alignment explanation
Indices: 3382918--3382984 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
3382908 CAGTAAAATA
*
3382918 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
3382952 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
3382985 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:3382958 original size:20 final size:20
Alignment explanation
Indices: 3382933--3382972 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3382923 CGTAAAATGA
*
3382933 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
3382953 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
3382973 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:3382988 original size:14 final size:15
Alignment explanation
Indices: 3382912--3382988 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
3382902 GATTGCCAGT
* *
3382912 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
3382926 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
3382940 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
3382960 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
3382975 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
3382989 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:3396226 original size:22 final size:23
Alignment explanation
Indices: 3396170--3396228 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
3396160 TTGAAGTCCG
3396170 GTAC-TAAATAATTATGAAATCT
1 GTACTTAAATAATTATGAAATCT
* *
3396192 GTATTTAAA-AATT-TTAAAGTCT
1 GTACTTAAATAATTATGAAA-TCT
3396214 GT-CTTAAATAATTAT
1 GTACTTAAATAATTAT
3396229 ACCAAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
21 9 0.30
22 16 0.53
23 5 0.17
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (23 bp):
GTACTTAAATAATTATGAAATCT
Found at i:3396950 original size:20 final size:21
Alignment explanation
Indices: 3396913--3396966 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 21
3396903 CCCGGCCTAT
**
3396913 TTTTAATAAATACCAAAAATTTA
1 TTTTAA-AAATA-CAAAAAAATA
3396936 TTTTAAAAATA-AAAAAAATA
1 TTTTAAAAATACAAAAAAATA
3396956 TTTTAAAAATA
1 TTTTAAAAATA
3396967 TTTTAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 18 0.62
22 5 0.17
23 6 0.21
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (21 bp):
TTTTAAAAATACAAAAAAATA
Found at i:3396969 original size:31 final size:32
Alignment explanation
Indices: 3396934--3397008 Score: 127
Period size: 30 Copynumber: 2.4 Consensus size: 32
3396924 ACCAAAAATT
3396934 TATTTTAAAAATAAAAAAAATATTTTAAAAA-
1 TATTTTAAAAATAAAAAAAATATTTTAAAAAG
*
3396965 TATTTT-AAAATTAAAAAAATATTTTAAAAAG
1 TATTTTAAAAATAAAAAAAATATTTTAAAAAG
3396996 TATTTTAAAAATA
1 TATTTTAAAAATA
3397009 TTTTAAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
30 23 0.57
31 12 0.30
32 5 0.12
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (32 bp):
TATTTTAAAAATAAAAAAAATATTTTAAAAAG
Found at i:3396999 original size:12 final size:11
Alignment explanation
Indices: 3396949--3397016 Score: 88
Period size: 11 Copynumber: 6.4 Consensus size: 11
3396939 TAAAAATAAA
3396949 AAAAATATTTT
1 AAAAATATTTT
3396960 AAAAATATTTT
1 AAAAATATTTT
**
3396971 --AAA-ATTAA
1 AAAAATATTTT
3396979 AAAAATATTTT
1 AAAAATATTTT
3396990 AAAAAGTATTTT
1 AAAAA-TATTTT
3397002 AAAAATATTTT
1 AAAAATATTTT
3397013 AAAA
1 AAAA
3397017 TTAAAAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
8 3 0.06
9 3 0.06
10 3 0.06
11 29 0.59
12 11 0.22
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:3397085 original size:18 final size:17
Alignment explanation
Indices: 3397040--3397085 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
3397030 AAAAGTATTT
*
3397040 TAAAAATATTTTAAAAT
1 TAAAAATATTTTAAAAA
*
3397057 TAAAAAAATTTTAAAAAA
1 TAAAAATATTTT-AAAAA
*
3397075 TAAATATATTT
1 TAAAAATATTT
3397086 ATTATATCGG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAAAATATTTTAAAAA
Found at i:3414839 original size:3 final size:3
Alignment explanation
Indices: 3414831--3414860 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
3414821 GCTAAAATGT
3414831 TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3414861 AACCGATCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3414850 original size:14 final size:14
Alignment explanation
Indices: 3414831--3414857 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3414821 GCTAAAATGT
3414831 TTATTATTATTATA
1 TTATTATTATTATA
3414845 TTATTATTATTAT
1 TTATTATTATTAT
3414858 TATAACCGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTATTATTATA
Found at i:3416883 original size:17 final size:16
Alignment explanation
Indices: 3416869--3416898 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3416859 ACTGAGAATT
3416869 AAAA-AAAAAAAAGAA
1 AAAAGAAAAAAAAGAA
3416884 AAAAGAAAAAAAAGA
1 AAAAGAAAAAAAAGA
3416899 TACGATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAAAAGAA
Found at i:3423887 original size:15 final size:17
Alignment explanation
Indices: 3423857--3423889 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
3423847 AATGATTCGT
3423857 TAATCAACTCATCATCA
1 TAATCAACTCATCATCA
3423874 TAATCAA-T-ATCATCA
1 TAATCAACTCATCATCA
3423889 T
1 T
3423890 CCTCAATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 1 0.06
17 7 0.44
ACGTcount: A:0.42, C:0.24, G:0.00, T:0.33
Consensus pattern (17 bp):
TAATCAACTCATCATCA
Found at i:3425092 original size:14 final size:14
Alignment explanation
Indices: 3425069--3425103 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
3425059 ATATAAAGAT
*
3425069 AAATTATTTATATTA
1 AAATT-TTTATATGA
3425084 AAATTTTTATATGA
1 AAATTTTTATATGA
3425098 AAATTT
1 AAATTT
3425104 ATCTTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (14 bp):
AAATTTTTATATGA
Found at i:3430178 original size:5 final size:5
Alignment explanation
Indices: 3430164--3430201 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
3430154 ACAATATCTC
*
3430164 TTTCT TTTCT CTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
3430202 TATTTCCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTCT
Found at i:3434835 original size:23 final size:24
Alignment explanation
Indices: 3434787--3434846 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 24
3434777 AACATAATTT
*
3434787 AAAAT-TTTATATACGACAATTGA
1 AAAATATTTATTTACGACAATTGA
* *
3434810 AAAATATTTATTTACG-CACTTTA
1 AAAATATTTATTTACGACAATTGA
*
3434833 AAAATAATTATTTA
1 AAAATATTTATTTA
3434847 TTTAATTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 23 0.72
24 9 0.28
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (24 bp):
AAAATATTTATTTACGACAATTGA
Found at i:3438008 original size:12 final size:12
Alignment explanation
Indices: 3437991--3438046 Score: 57
Period size: 11 Copynumber: 4.9 Consensus size: 12
3437981 ACTAATCCTA
3437991 TCTCAAATTTCC
1 TCTCAAATTTCC
*
3438003 TCTC-AATTTCT
1 TCTCAAATTTCC
*
3438014 TCT-AAATTTGC
1 TCTCAAATTTCC
3438025 TCTC-AATTTCC
1 TCTCAAATTTCC
3438036 T-TCAAAATTTC
1 TCTC-AAATTTC
3438047 TCTAAAATCC
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
10 2 0.06
11 24 0.67
12 10 0.28
ACGTcount: A:0.25, C:0.27, G:0.02, T:0.46
Consensus pattern (12 bp):
TCTCAAATTTCC
Found at i:3438020 original size:22 final size:23
Alignment explanation
Indices: 3437995--3438046 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
3437985 ATCCTATCTC
*
3437995 AAATTTCCTCTCAATTT-CTTCT
1 AAATTTCCTCTCAATTTCCTTCA
*
3438017 AAATTTGCTCTCAATTTCCTTCA
1 AAATTTCCTCTCAATTTCCTTCA
3438040 AAATTTC
1 AAATTTC
3438047 TCTAAAATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 16 0.62
23 10 0.38
ACGTcount: A:0.27, C:0.25, G:0.02, T:0.46
Consensus pattern (23 bp):
AAATTTCCTCTCAATTTCCTTCA
Found at i:3439881 original size:27 final size:27
Alignment explanation
Indices: 3439843--3439897 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
3439833 CAACCTGTGT
*
3439843 TACCAACGCAACCGT-CTTTTTAGATGA
1 TACCAACGCAACC-TCCTTTTCAGATGA
*
3439870 TACCCACGCAACCTCCTTTTCAGATGA
1 TACCAACGCAACCTCCTTTTCAGATGA
3439897 T
1 T
3439898 GCTGATGAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 24 0.96
ACGTcount: A:0.27, C:0.31, G:0.13, T:0.29
Consensus pattern (27 bp):
TACCAACGCAACCTCCTTTTCAGATGA
Found at i:3441919 original size:126 final size:124
Alignment explanation
Indices: 3441659--3442132 Score: 628
Period size: 126 Copynumber: 3.8 Consensus size: 124
3441649 CAAACATGTT
* * *
3441659 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATTTTGCTA
1 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCA-TCTGCTT
** * * *
3441724 GAAGC-AATTTTATACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTCCAGGACCA
65 GAAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACCA
*
3441783 ACTGTAGCAAAAGTGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCA-AATAGCATGCTGCT
1 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAA-AGCAT-CTGCT
* * * * * *
3441847 TGCAGCGTTGTTTTATACTATTTGCTCAGAAACATAAACTCAAAATTATTTTTTCAGGACCT
64 TGAAGCGTT-TTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACCA
* * *
3441909 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGACTTCACAAATTCTTCTTATAAAGCATCTTGCTT
1 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATC-TGCTT
* *
3441974 GAAGCGTTTTTTAAACTATTTGCTCAAAAACGTCAACTCGAAATTATTTCTTTCAAGACCA
65 GAAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTTCAGGACCA
* * * * * *
3442035 ACTGTAGTAAAAGCGCGTTCATGAGGGCCCGATTTCACAAATTCTTCTCACAAAGCATCCTGTTT
1 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCAT-CTGCTT
*
3442100 GAAGCGTTTTTTAAACTATTTGCTTAGAAACGT
65 GAAGCGTTTTTTAAACTATTTGCTCAGAAACGT
3442133 AGGCGTGACT
Statistics
Matches: 306, Mismatches: 36, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
123 3 0.01
124 60 0.20
125 37 0.12
126 203 0.66
127 3 0.01
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (124 bp):
ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCTGCTTG
AAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACCA
Found at i:3443070 original size:31 final size:31
Alignment explanation
Indices: 3442992--3443076 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 31
3442982 GACTAATATT
* *
3442992 TTATGTATCATTATAATAAATTATTTAAATA
1 TTATTTATCATTATATTAAATTATTTAAATA
* * * *
3443023 TAATTTATCATAATATTAAATTATTTAATTC
1 TTATTTATCATTATATTAAATTATTTAAATA
*
3443054 TTATTTATTATTATATTTAAATT
1 TTATTTATCATTATA-TTAAATT
3443077 TGTAAAAAGG
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 37 0.84
32 7 0.16
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (31 bp):
TTATTTATCATTATATTAAATTATTTAAATA
Found at i:3450417 original size:31 final size:31
Alignment explanation
Indices: 3450311--3450442 Score: 138
Period size: 31 Copynumber: 4.1 Consensus size: 31
3450301 TTAATAAAAA
3450311 AAATATAAATACTACATTAAAAATACGTATG
1 AAATATAAATACTACATTAAAAATACGTATG
* * * * * * * * *
3450342 AAATTTAACTACCAAATTATATATTAAGCTTTAA
1 AAATATAAATACTACATTA-AAAATACG-TAT-G
*
3450376 AAATCGTAAATACTACATTAAAAATACGTATG
1 AAAT-ATAAATACTACATTAAAAATACGTATG
3450408 AAATATAAATACTACATTAAAAATACGTATG
1 AAATATAAATACTACATTAAAAATACGTATG
3450439 AAAT
1 AAAT
3450443 TTAACTACCA
Statistics
Matches: 78, Mismatches: 19, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
31 45 0.58
32 9 0.12
33 4 0.05
34 9 0.12
35 11 0.14
ACGTcount: A:0.52, C:0.11, G:0.06, T:0.31
Consensus pattern (31 bp):
AAATATAAATACTACATTAAAAATACGTATG
Found at i:3450529 original size:97 final size:96
Alignment explanation
Indices: 3450311--3450507 Score: 326
Period size: 97 Copynumber: 2.1 Consensus size: 96
3450301 TTAATAAAAA
3450311 AAATATAAATACTACATTAAAAATACGTATGAAATTTAACTACCAAATTATATATTAAGCTTTAA
1 AAATATAAATACTACATTAAAAATACGTATGAAATTTAACTACCAAATTATATATTAAGCTTTAA
* *
3450376 AAATCGTAAATACTACATTAAAAATACGTATG
66 AAATCGTAAAAAATACATTAAAAATA-GTATG
3450408 AAATATAAATACTACATTAAAAATACGTATGAAATTTAACTACCAAATTATATATTAAGCTTTAA
1 AAATATAAATACTACATTAAAAATACGTATGAAATTTAACTACCAAATTATATATTAAGCTTTAA
* **
3450473 AAATCGTAAAAAAT-CGTTATTAAT-GTATG
66 AAATCGTAAAAAATACATTAAAAATAGTATG
3450502 AAATAT
1 AAATAT
3450508 GATCCTATAT
Statistics
Matches: 95, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
94 11 0.12
96 7 0.07
97 77 0.81
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (96 bp):
AAATATAAATACTACATTAAAAATACGTATGAAATTTAACTACCAAATTATATATTAAGCTTTAA
AAATCGTAAAAAATACATTAAAAATAGTATG
Found at i:3455737 original size:71 final size:71
Alignment explanation
Indices: 3455621--3455766 Score: 292
Period size: 71 Copynumber: 2.1 Consensus size: 71
3455611 TACCCTATTT
3455621 TGTTAGAGGCTTCAGAGTGTGGCTTTTTTTCAAAAATAAATATTTAAGCCAAATGAACTAGTAGT
1 TGTTAGAGGCTTCAGAGTGTGGCTTTTTTTCAAAAATAAATATTTAAGCCAAATGAACTAGTAGT
3455686 AAATCA
66 AAATCA
3455692 TGTTAGAGGCTTCAGAGTGTGGCTTTTTTTCAAAAATAAATATTTAAGCCAAATGAACTAGTAGT
1 TGTTAGAGGCTTCAGAGTGTGGCTTTTTTTCAAAAATAAATATTTAAGCCAAATGAACTAGTAGT
3455757 AAATCA
66 AAATCA
3455763 TGTT
1 TGTT
3455767 TACTTACCTT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 75 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (71 bp):
TGTTAGAGGCTTCAGAGTGTGGCTTTTTTTCAAAAATAAATATTTAAGCCAAATGAACTAGTAGT
AAATCA
Found at i:3467207 original size:27 final size:27
Alignment explanation
Indices: 3467139--3467210 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
3467129 GGTGGAGGGC
*
3467139 CTGCCACAGGCAGCACCAAAGATGCCA
1 CTGCCACAGGCGGCACCAAAGATGCCA
* * * *
3467166 GTGGCA-AAGCTGGCACCAAAGGTGCCA
1 CTGCCACAGGC-GGCACCAAAGATGCCA
3467193 CTGCCACAGGCGGCACCA
1 CTGCCACAGGCGGCACCA
3467211 CCCCCATTAT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
26 3 0.09
27 29 0.83
28 3 0.09
ACGTcount: A:0.29, C:0.35, G:0.28, T:0.08
Consensus pattern (27 bp):
CTGCCACAGGCGGCACCAAAGATGCCA
Found at i:3467266 original size:19 final size:20
Alignment explanation
Indices: 3467242--3467283 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
3467232 GATTCGACTG
*
3467242 AAGGAGAAGAAA-AAAAGGA
1 AAGGAGAAGAAAGAAAAAGA
3467261 AAGGAGAAGAAAGAAAAAGA
1 AAGGAGAAGAAAGAAAAAGA
3467281 AAG
1 AAG
3467284 AAAAGGAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (20 bp):
AAGGAGAAGAAAGAAAAAGA
Found at i:3467290 original size:30 final size:29
Alignment explanation
Indices: 3467248--3467329 Score: 112
Period size: 30 Copynumber: 2.8 Consensus size: 29
3467238 ACTGAAGGAG
3467248 AAGAAA-AAAAGGAAAGGAGAAGAAAGAAA
1 AAGAAAGAAAAGGAAAGGAGAAG-AAGAAA
*
3467277 AAGAAAGAAAAGGAAAGGAGAAGAAGAAG
1 AAGAAAGAAAAGGAAAGGAGAAGAAGAAA
* *
3467306 AAGAAGGAGAAGGAGAAGGAGAAG
1 AAGAAAGAAAAGGA-AAGGAGAAG
3467330 GAGGCGCGGG
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
29 23 0.48
30 25 0.52
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (29 bp):
AAGAAAGAAAAGGAAAGGAGAAGAAGAAA
Found at i:3467332 original size:6 final size:6
Alignment explanation
Indices: 3467286--3467332 Score: 69
Period size: 6 Copynumber: 8.0 Consensus size: 6
3467276 AAAGAAAGAA
* *
3467286 AAGGA- AAGGAG AAGAAG AAGAAG AAGGAG AAGGAG AAGGAG AAGGAG
1 AAGGAG AAGGAG AAGGAG AAGGAG AAGGAG AAGGAG AAGGAG AAGGAG
3467333 GCGCGGGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
5 5 0.13
6 34 0.87
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (6 bp):
AAGGAG
Found at i:3467431 original size:20 final size:19
Alignment explanation
Indices: 3467406--3467444 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
3467396 AAAAGAAAGA
3467406 TAATTTTTTTGGTATTATTT
1 TAATTTTTTT-GTATTATTT
3467426 TAATTTTTTTGTATTATTT
1 TAATTTTTTTGTATTATTT
3467445 ATGTAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.72
Consensus pattern (19 bp):
TAATTTTTTTGTATTATTT
Found at i:3467652 original size:17 final size:17
Alignment explanation
Indices: 3467632--3467664 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3467622 GTTTATGAAA
*
3467632 AAATAAAATACGAAAAG
1 AAATAAAAAACGAAAAG
3467649 AAATAAAAAACGAAAA
1 AAATAAAAAACGAAAA
3467665 TAGTATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.06, G:0.09, T:0.09
Consensus pattern (17 bp):
AAATAAAAAACGAAAAG
Found at i:3469542 original size:12 final size:12
Alignment explanation
Indices: 3469528--3469585 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
3469518 GACAGATCCT
*
3469528 GATCCCGAGCCT
1 GATCCCGAGCCA
* * *
3469540 GATCTCGAACCG
1 GATCCCGAGCCA
* *
3469552 GAGCCCAAGCCA
1 GATCCCGAGCCA
*
3469564 GAGCCCGAGCCA
1 GATCCCGAGCCA
3469576 GATCCCGAGC
1 GATCCCGAGC
3469586 AATCACATTC
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.24, C:0.40, G:0.28, T:0.09
Consensus pattern (12 bp):
GATCCCGAGCCA
Found at i:3471296 original size:76 final size:77
Alignment explanation
Indices: 3471180--3471326 Score: 217
Period size: 76 Copynumber: 1.9 Consensus size: 77
3471170 TAGTTTTTTT
3471180 ACTAAAAATAATACTAACTAACAATAATAATTAGGGTTTTACTAAAAATAATAACTAACAATAAT
1 ACTAAAAATAATACTAACTAACAATAATAATTAGGGTTTTACTAAAAATAATAACTAACAATAAT
3471245 -ATAATGTAAAA
66 AATAATGTAAAA
* * *** *
3471256 ACTAATAATCATACTAACTAA-AATAATAATTAGGGTTTTTACTAATCCTAATAACTAACCATAA
1 ACTAAAAATAATACTAACTAACAATAATAATTAGGG-TTTTACTAAAAATAATAACTAACAATAA
3471320 TAATAAT
65 TAATAAT
3471327 ATTAGTTTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
75 14 0.22
76 44 0.70
77 5 0.08
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (77 bp):
ACTAAAAATAATACTAACTAACAATAATAATTAGGGTTTTACTAAAAATAATAACTAACAATAAT
AATAATGTAAAA
Found at i:3472598 original size:13 final size:14
Alignment explanation
Indices: 3472580--3472608 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3472570 GTACTACAAG
3472580 ATTATTTT-TTTAA
1 ATTATTTTATTTAA
3472593 ATTATTTTATTTAA
1 ATTATTTTATTTAA
3472607 AT
1 AT
3472609 GTCTATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
ATTATTTTATTTAA
Found at i:3472982 original size:27 final size:26
Alignment explanation
Indices: 3472947--3473010 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
3472937 TTAATGAACT
*
3472947 TTAGCGCACTCTTTGAT-TATTAGCACG
1 TTAGTGCACTC-TTGATAT-TTAGCACG
*
3472974 TTGGTGCACTC-TGATATTTAGCACG
1 TTAGTGCACTCTTGATATTTAGCACG
*
3472999 TTAGTGCTCTCT
1 TTAGTGCACTCT
3473011 GTTTAGCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
25 21 0.68
26 1 0.03
27 9 0.29
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.39
Consensus pattern (26 bp):
TTAGTGCACTCTTGATATTTAGCACG
Found at i:3473018 original size:22 final size:22
Alignment explanation
Indices: 3472966--3473057 Score: 96
Period size: 22 Copynumber: 4.0 Consensus size: 22
3472956 TCTTTGATTA
* *
3472966 TTAGCACGTTGGTGCACTCTGATAT
1 TTAGCACGTTAGTGCTCTCTG---T
3472991 TTAGCACGTTAGTGCTCTCTGT
1 TTAGCACGTTAGTGCTCTCTGT
*
3473013 TTAGCACATCT-GTGCTCTCTGT
1 TTAGCACGT-TAGTGCTCTCTGT
* *
3473035 ATAGCACTTTAGTGCTCTCTGT
1 TTAGCACGTTAGTGCTCTCTGT
3473057 T
1 T
3473058 CATTAGTGCA
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
21 1 0.02
22 38 0.64
23 1 0.02
25 19 0.32
ACGTcount: A:0.16, C:0.23, G:0.21, T:0.40
Consensus pattern (22 bp):
TTAGCACGTTAGTGCTCTCTGT
Found at i:3474612 original size:18 final size:18
Alignment explanation
Indices: 3474564--3474612 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
3474554 AAAAAAACTT
*
3474564 AAATCTTTTTTAGGGCCAA
1 AAATC-TTTTTATGGCCAA
*
3474583 AAACCTTTTTATGG-CAA
1 AAATCTTTTTATGGCCAA
3474600 AAATCTTTATTAT
1 AAATCTTT-TTAT
3474613 TTTTTTCTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 10 0.38
18 12 0.46
19 4 0.15
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (18 bp):
AAATCTTTTTATGGCCAA
Found at i:3478666 original size:11 final size:11
Alignment explanation
Indices: 3478650--3478683 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
3478640 CCCCCCCCCG
3478650 AAAAAAAAAGAA
1 AAAAAAAAAG-A
3478662 AAAAAAAAAGA
1 AAAAAAAAAGA
*
3478673 AAAAGAAAAGA
1 AAAAAAAAAGA
3478684 GAGGCTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:3478667 original size:12 final size:12
Alignment explanation
Indices: 3478650--3478681 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
3478640 CCCCCCCCCG
3478650 AAAAAAAAAGAA
1 AAAAAAAAAGAA
3478662 AAAAAAAAAGAA
1 AAAAAAAAAGAA
3478674 AAAGAAAA
1 AAA-AAAA
3478682 GAGAGGCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:3485053 original size:21 final size:21
Alignment explanation
Indices: 3485027--3485100 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
3485017 CATATTTTAG
3485027 ATATAAAATAATTA-AATATAA
1 ATAT-AAATAATTATAATATAA
*
3485048 ATATAAATAATTATATTATAA
1 ATATAAATAATTATAATATAA
* *
3485069 ATATTAATTATTATTAAT-TAA
1 ATATAAATAATTA-TAATATAA
*
3485090 TTATATAATAA
1 ATATA-AATAA
3485101 CCCAACAACA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
20 9 0.21
21 27 0.63
22 7 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATATAAATAATTATAATATAA
Found at i:3495651 original size:24 final size:24
Alignment explanation
Indices: 3495624--3495670 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
3495614 CTCTTGAAAC
*
3495624 TTTAGTCAATACCCAAATAAGTCA
1 TTTAATCAATACCCAAATAAGTCA
* * *
3495648 TTTAATTAGTGCCCAAATAAGTC
1 TTTAATCAATACCCAAATAAGTC
3495671 CTTAATCTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (24 bp):
TTTAATCAATACCCAAATAAGTCA
Found at i:3500199 original size:24 final size:24
Alignment explanation
Indices: 3500165--3500216 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
3500155 TTCCTAGAAG
* * *
3500165 ATTTAGTATTTGTGAGTATAATAT
1 ATTTAGCATTTATGAGCATAATAT
*
3500189 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATGAGCATAATAT
3500213 ATTT
1 ATTT
3500217 CACATTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCATAATAT
Found at i:3500222 original size:24 final size:24
Alignment explanation
Indices: 3500182--3500228 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3500172 ATTTGTGAGT
*
3500182 ATAATATATTTAGCATTTATTAGC
1 ATAATATATTTAGCATTGATTAGC
3500206 ATAATATATTTCA-CATTGATTAG
1 ATAATATATTT-AGCATTGATTAG
3500229 AATTAGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.45
Consensus pattern (24 bp):
ATAATATATTTAGCATTGATTAGC
Found at i:3504643 original size:16 final size:16
Alignment explanation
Indices: 3504605--3504643 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3504595 GTCAAAAGGT
* *
3504605 GAAAAAAAAATGAAAG
1 GAAAAATAAATGAAAA
*
3504621 GATAAATAAATGAAAA
1 GAAAAATAAATGAAAA
3504637 GAAAAAT
1 GAAAAAT
3504644 TGCAAATAGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (16 bp):
GAAAAATAAATGAAAA
Found at i:3512402 original size:30 final size:32
Alignment explanation
Indices: 3512365--3512426 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
3512355 AAGATTTAAG
*
3512365 AAAAA-AGAGAGCTTAGATTAGAAACATACTT
1 AAAAAGAGAGAGCTCAGATTAGAAACATACTT
*
3512396 AAAAAGAGAGAGCTCAGATTAGTAACATACT
1 AAAAAGAGAGAGCTCAGATTAGAAACATACT
3512427 CATTTTAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 5 0.18
32 23 0.82
ACGTcount: A:0.50, C:0.11, G:0.18, T:0.21
Consensus pattern (32 bp):
AAAAAGAGAGAGCTCAGATTAGAAACATACTT
Found at i:3512626 original size:21 final size:21
Alignment explanation
Indices: 3512596--3512639 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
3512586 TCCTAATTTT
3512596 AAATCTAAACC-TAAACACTA
1 AAATCTAAACCTTAAACACTA
*
3512616 AAATCATAAACCTTAAGCACTA
1 AAATC-TAAACCTTAAACACTA
3512638 AA
1 AA
3512640 CTAAAAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 6 0.29
22 10 0.48
ACGTcount: A:0.55, C:0.23, G:0.02, T:0.20
Consensus pattern (21 bp):
AAATCTAAACCTTAAACACTA
Found at i:3512648 original size:22 final size:23
Alignment explanation
Indices: 3512623--3512670 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
3512613 CTAAAATCAT
3512623 AAACCTTAAGCACTAAAC-TAAA
1 AAACCTTAAGCACTAAACTTAAA
**
3512645 AAA-CTTGTGCACTAAACTTAAA
1 AAACCTTAAGCACTAAACTTAAA
3512667 AAAC
1 AAAC
3512671 TTCGAACCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.52, C:0.21, G:0.06, T:0.21
Consensus pattern (23 bp):
AAACCTTAAGCACTAAACTTAAA
Found at i:3512658 original size:21 final size:22
Alignment explanation
Indices: 3512632--3512672 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
3512622 TAAACCTTAA
3512632 GCACTAAAC-TAAAAAACTTGT
1 GCACTAAACTTAAAAAACTTGT
3512653 GCACTAAACTTAAAAAACTT
1 GCACTAAACTTAAAAAACTT
3512673 CGAACCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.49, C:0.20, G:0.07, T:0.24
Consensus pattern (22 bp):
GCACTAAACTTAAAAAACTTGT
Found at i:3516322 original size:71 final size:71
Alignment explanation
Indices: 3516206--3516418 Score: 408
Period size: 71 Copynumber: 3.0 Consensus size: 71
3516196 TATTCATTAA
*
3516206 TTACAAAAGGTAGTACTAAATTTATCAGATAAACTTTTAAGAAAAAGACACTGTAAGATAGTCCA
1 TTACAAAAGGTAGTACTAAATTTATCAGATAAACTTATAAGAAAAAGACACTGTAAGATAGTCCA
3516271 CAAGAC
66 CAAGAC
3516277 TTACAAAAGGTAGTACTAAATTTATCAGATAAACTTATAAGAAAAAGACACTGTAAGATAGTCCA
1 TTACAAAAGGTAGTACTAAATTTATCAGATAAACTTATAAGAAAAAGACACTGTAAGATAGTCCA
3516342 CAAGAC
66 CAAGAC
*
3516348 TTACAAAAGGTAGTACTAAATTTATCATATAAACTTATAAGAAAAAGACACTGTAAGATAGTCCA
1 TTACAAAAGGTAGTACTAAATTTATCAGATAAACTTATAAGAAAAAGACACTGTAAGATAGTCCA
3516413 CAAGAC
66 CAAGAC
3516419 CCATTCCTTT
Statistics
Matches: 140, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 140 1.00
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (71 bp):
TTACAAAAGGTAGTACTAAATTTATCAGATAAACTTATAAGAAAAAGACACTGTAAGATAGTCCA
CAAGAC
Found at i:3516350 original size:37 final size:37
Alignment explanation
Indices: 3516309--3516418 Score: 86
Period size: 37 Copynumber: 3.1 Consensus size: 37
3516299 TATCAGATAA
3516309 ACTTATAAGAAAAAGACACTGTAAGATAGTCCACAAG
1 ACTTATAAGAAAAAGACACTGTAAGATAGTCCACAAG
* ** * * ** * *
3516346 ACTTACAA-AAGGTAG-TACT-AAATTTA-T-CATATAA
1 ACTTATAAGAA-AAAGACACTGTAAGATAGTCCACA-AG
3516380 ACTTATAAGAAAAAGACACTGTAAGATAGTCCACAAG
1 ACTTATAAGAAAAAGACACTGTAAGATAGTCCACAAG
3516417 AC
1 AC
3516419 CCATTCCTTT
Statistics
Matches: 48, Mismatches: 18, Indels: 14
0.60 0.22 0.17
Matches are distributed among these distances:
33 3 0.06
34 11 0.23
35 9 0.19
36 9 0.19
37 13 0.27
38 3 0.06
ACGTcount: A:0.48, C:0.15, G:0.14, T:0.23
Consensus pattern (37 bp):
ACTTATAAGAAAAAGACACTGTAAGATAGTCCACAAG
Found at i:3523689 original size:20 final size:21
Alignment explanation
Indices: 3523635--3523689 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
3523625 AGATAAAAAC
3523635 AGAAAGAAAA--AGAAA-GAA
1 AGAAAGAAAAGGAGAAAGGAA
3523653 AGAAAGAAAAGGA-AAAGGAA
1 AGAAAGAAAAGGAGAAAGGAA
*
3523673 AGAAAG-GAAGGAGAAAG
1 AGAAAGAAAAGGAGAAAG
3523690 CCATTGCCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 10 0.31
19 8 0.25
20 14 0.44
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (21 bp):
AGAAAGAAAAGGAGAAAGGAA
Found at i:3546476 original size:2 final size:2
Alignment explanation
Indices: 3546469--3546496 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3546459 TTAAAATTAA
3546469 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3546497 TAAAGATTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3548796 original size:23 final size:23
Alignment explanation
Indices: 3548766--3548811 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
3548756 AGAAAGCCCG
3548766 CATAAATGAAAGTGATATTAAAA
1 CATAAATGAAAGTGATATTAAAA
3548789 CATAAATGAAAGTGATATTAAAA
1 CATAAATGAAAGTGATATTAAAA
3548812 ATATTCCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.57, C:0.04, G:0.13, T:0.26
Consensus pattern (23 bp):
CATAAATGAAAGTGATATTAAAA
Found at i:3556474 original size:13 final size:12
Alignment explanation
Indices: 3556444--3556476 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
3556434 TAACACTTTA
3556444 AAAAAATTATTT
1 AAAAAATTATTT
3556456 -AAAAATTATATT
1 AAAAAATTAT-TT
3556468 AAAAAATTA
1 AAAAAATTA
3556477 ACATTTACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.47
12 2 0.11
13 8 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
AAAAAATTATTT
Found at i:3557645 original size:29 final size:30
Alignment explanation
Indices: 3557564--3557645 Score: 87
Period size: 31 Copynumber: 2.7 Consensus size: 30
3557554 GATTAAATCA
3557564 AAATTAAAGTTGTAA-GTATATATTTGAACC
1 AAATTAAAGTT-TAATGTATATATTTGAACC
* * * * *
3557594 ACAACTAGAGTTTCATGTGTATATTTGCACC
1 A-AATTAAAGTTTAATGTATATATTTGAACC
3557625 AAATTAAAG-TTAATGTATATA
1 AAATTAAAGTTTAATGTATATA
3557646 ATTACATATT
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
29 10 0.24
30 9 0.22
31 22 0.54
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (30 bp):
AAATTAAAGTTTAATGTATATATTTGAACC
Found at i:3561405 original size:2 final size:2
Alignment explanation
Indices: 3561400--3561439 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3561390 GGGGGGGCTA
3561400 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3561440 GGGGGAGAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3561708 original size:17 final size:17
Alignment explanation
Indices: 3561688--3561720 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3561678 GTATTTAATA
3561688 AATA-TAATATAAAAAAT
1 AATACTAATA-AAAAAAT
3561705 AATACTAATAAAAAAA
1 AATACTAATAAAAAAA
3561721 AATTTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AATACTAATAAAAAAAT
Found at i:3561721 original size:18 final size:17
Alignment explanation
Indices: 3561688--3561721 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3561678 GTATTTAATA
*
3561688 AATATAATATAAAAAAT
1 AATATAATAAAAAAAAT
3561705 AATACTAATAAAAAAAA
1 AATA-TAATAAAAAAAA
3561722 ATTTAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AATATAATAAAAAAAAT
Found at i:3572304 original size:18 final size:18
Alignment explanation
Indices: 3572281--3572322 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
3572271 TCTAGATCTT
3572281 CAATGAATCTTATTATAC
1 CAATGAATCTTATTATAC
* *
3572299 CAATG-A-CTTGTTATAT
1 CAATGAATCTTATTATAC
3572315 CAATGAAT
1 CAATGAAT
3572323 GTTTATCTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
16 13 0.65
17 2 0.10
18 5 0.25
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (18 bp):
CAATGAATCTTATTATAC
Found at i:3598661 original size:18 final size:17
Alignment explanation
Indices: 3598627--3598683 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
3598617 TGGACATTTT
3598627 AATTATTTTTGAAAAAA
1 AATTATTTTTGAAAAAA
*
3598644 AATTATTTTCT-TAAAAA
1 AATTATTTT-TGAAAAAA
3598661 AA--A-TTTTGAAAAAA
1 AATTATTTTTGAAAAAA
3598675 AA-TATTTTT
1 AATTATTTTT
3598684 TTGCTGATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
13 1 0.03
14 10 0.29
15 2 0.06
16 4 0.12
17 16 0.47
18 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (17 bp):
AATTATTTTTGAAAAAA
Found at i:3598674 original size:15 final size:15
Alignment explanation
Indices: 3598633--3598682 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
3598623 TTTTAATTAT
3598633 TTTTGAAAAAAAATTA
1 TTTTGAAAAAAAA-TA
**
3598649 TTTTCTTAAAAAAA-A
1 TTTT-GAAAAAAAATA
3598664 TTTTGAAAAAAAATA
1 TTTTGAAAAAAAATA
3598679 TTTT
1 TTTT
3598683 TTTGCTGATG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
14 7 0.25
15 10 0.36
16 4 0.14
17 7 0.25
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (15 bp):
TTTTGAAAAAAAATA
Found at i:3607175 original size:22 final size:22
Alignment explanation
Indices: 3607146--3607201 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
3607136 TGCACTAATG
*
3607146 AACAGAGAGCACTGAAGTGCTA
1 AACAGAGAGCACAGAAGTGCTA
* *
3607168 TACAGAGAGCACAGATGTGCTA
1 AACAGAGAGCACAGAAGTGCTA
3607190 AACAGAGAGCAC
1 AACAGAGAGCAC
3607202 CAACGTGCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.41, C:0.20, G:0.27, T:0.12
Consensus pattern (22 bp):
AACAGAGAGCACAGAAGTGCTA
Found at i:3607209 original size:22 final size:21
Alignment explanation
Indices: 3607146--3607212 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 21
3607136 TGCACTAATG
*
3607146 AACAGAGAGCACTGAAGTGCTA
1 AACAGAGAGCAC-CAAGTGCTA
*
3607168 TACAGAGAGCA-CAGATGTGCTA
1 AACAGAGAGCACCA-A-GTGCTA
3607190 AACAGAGAGCACCAACGTGCTA
1 AACAGAGAGCACCAA-GTGCTA
3607212 A
1 A
3607213 TAATCAGAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
20 1 0.03
21 1 0.03
22 34 0.89
23 2 0.05
ACGTcount: A:0.40, C:0.21, G:0.25, T:0.13
Consensus pattern (21 bp):
AACAGAGAGCACCAAGTGCTA
Found at i:3608215 original size:5 final size:5
Alignment explanation
Indices: 3608205--3608237 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
3608195 TTATCTCTTT
3608205 TATAA TATAA TATAA TATAA TAT-A TATAA TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATA
3608238 TAACTTAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:3624826 original size:14 final size:14
Alignment explanation
Indices: 3624788--3624831 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
3624778 CATTTTAGTA
3624788 AATAAT-TTTAAAT
1 AATAATATTTAAAT
* *
3624801 ACATATTATTTAAGT
1 A-ATAATATTTAAAT
3624816 AATAATATTTAAAT
1 AATAATATTTAAAT
3624830 AA
1 AA
3624832 ATAAAAAAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
13 1 0.04
14 17 0.68
15 7 0.28
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (14 bp):
AATAATATTTAAAT
Found at i:3626752 original size:17 final size:18
Alignment explanation
Indices: 3626724--3626757 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3626714 ATCGGCTAAT
*
3626724 AATAAGATATTATTTAAA
1 AATAAGATATTAGTTAAA
3626742 AATAA-ATATTAGTTAA
1 AATAAGATATTAGTTAA
3626758 TATTTATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
AATAAGATATTAGTTAAA
Found at i:3633554 original size:6 final size:6
Alignment explanation
Indices: 3633543--3633574 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
3633533 TAGTATCATT
3633543 AATTAA AATTAA AATTAA AATTAA AATTAA AA
1 AATTAA AATTAA AATTAA AATTAA AATTAA AA
3633575 GAAAAAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AATTAA
Found at i:3633580 original size:18 final size:18
Alignment explanation
Indices: 3633543--3633580 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3633533 TAGTATCATT
**
3633543 AATTAAAATTAAAATTAA
1 AATTAAAATTAAAAGAAA
3633561 AATTAAAATTAAAAGAAA
1 AATTAAAATTAAAAGAAA
3633579 AA
1 AA
3633581 GAAAAAGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (18 bp):
AATTAAAATTAAAAGAAA
Found at i:3634717 original size:30 final size:31
Alignment explanation
Indices: 3634681--3634741 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
3634671 AGTTTTCAGT
* * *
3634681 AATATTTAA-TATTAATAAATATTTGAATTA
1 AATATTTAATTACTAACAAATATTTAAATTA
3634711 AATATTTAATTACTAACAAATATTTAAATTA
1 AATATTTAATTACTAACAAATATTTAAATTA
3634742 GTTCACAACG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 9 0.33
31 18 0.67
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (31 bp):
AATATTTAATTACTAACAAATATTTAAATTA
Found at i:3635788 original size:14 final size:14
Alignment explanation
Indices: 3635769--3635798 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3635759 GCTACCATTT
3635769 TACTATTATGTTGC
1 TACTATTATGTTGC
*
3635783 TACTATTTTGTTGC
1 TACTATTATGTTGC
3635797 TA
1 TA
3635799 TTGTTTGGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.13, T:0.53
Consensus pattern (14 bp):
TACTATTATGTTGC
Found at i:3638079 original size:15 final size:15
Alignment explanation
Indices: 3638056--3638085 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3638046 TGACAACAGA
3638056 TTTTCCTTTTCTTTT
1 TTTTCCTTTTCTTTT
*
3638071 TTTTTCTTTTCTTTT
1 TTTTCCTTTTCTTTT
3638086 AACGTACAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTCCTTTTCTTTT
Found at i:3641930 original size:7 final size:7
Alignment explanation
Indices: 3641906--3641943 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
3641896 GTTTTTATAG
3641906 AAAGAAA
1 AAAGAAA
3641913 AAA-AATGA
1 AAAGAA--A
3641921 AAAGAAA
1 AAAGAAA
3641928 AAAGAAA
1 AAAGAAA
3641935 AAAGAAA
1 AAAGAAA
3641942 AA
1 AA
3641944 CTATTATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
6 2 0.07
7 20 0.71
8 4 0.14
9 2 0.07
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (7 bp):
AAAGAAA
Found at i:3641935 original size:19 final size:19
Alignment explanation
Indices: 3641904--3641942 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3641894 TAGTTTTTAT
*
3641904 AGAAAGAAAAAAAATGAAA
1 AGAAAGAAAAAAAAAGAAA
3641923 AGAAA-AAAGAAAAAAGAAA
1 AGAAAGAAA-AAAAAAGAAA
3641942 A
1 A
3641943 ACTATTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (19 bp):
AGAAAGAAAAAAAAAGAAA
Found at i:3643663 original size:17 final size:17
Alignment explanation
Indices: 3643641--3643674 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3643631 TTATTTTAAT
*
3643641 TAAAAACTGGTTTAAAC
1 TAAAAACTGGATTAAAC
*
3643658 TAAAAAGTGGATTAAAC
1 TAAAAACTGGATTAAAC
3643675 AACCGTTTGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (17 bp):
TAAAAACTGGATTAAAC
Found at i:3678875 original size:151 final size:151
Alignment explanation
Indices: 3678601--3678904 Score: 599
Period size: 151 Copynumber: 2.0 Consensus size: 151
3678591 GGAGCGGTAA
3678601 TTGAACTTTAGAATGTTACCTTTCTTAGGACGGTAACAACAGCTGTCCTATGCCTGGTCAAATTG
1 TTGAACTTTAGAATGTTACCTTTCTTAGGACGGTAACAACAGCTGTCCTATGCCTGGTCAAATTG
3678666 ATTTAATGCTGTTGATGTTAACAATTTGTGGGAGGTTTTCACTCAGGGATGTCATGGCAAACATC
66 ATTTAATGCTGTTGATGTTAACAATTTGTGGGAGGTTTTCACTCAGGGATGTCATGGCAAACATC
3678731 TCTTGTATTTTATGAAAGTAT
131 TCTTGTATTTTATGAAAGTAT
3678752 TTGAACTTTAGAATGTTACCTTTCTTAGGACGGTAACAACAGCTGTCCTATGCCTGGTCAAATTG
1 TTGAACTTTAGAATGTTACCTTTCTTAGGACGGTAACAACAGCTGTCCTATGCCTGGTCAAATTG
*
3678817 ATTTAATGCTTTTGATGTTAACAATTTGTGGGAGGTTTTCACTCAGGGATGTCATGGCAAACATC
66 ATTTAATGCTGTTGATGTTAACAATTTGTGGGAGGTTTTCACTCAGGGATGTCATGGCAAACATC
3678882 TCTTGTATTTTATGAAAGTAT
131 TCTTGTATTTTATGAAAGTAT
3678903 TT
1 TT
3678905 TGTTGTTGCA
Statistics
Matches: 152, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
151 152 1.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (151 bp):
TTGAACTTTAGAATGTTACCTTTCTTAGGACGGTAACAACAGCTGTCCTATGCCTGGTCAAATTG
ATTTAATGCTGTTGATGTTAACAATTTGTGGGAGGTTTTCACTCAGGGATGTCATGGCAAACATC
TCTTGTATTTTATGAAAGTAT
Found at i:3692925 original size:28 final size:28
Alignment explanation
Indices: 3692885--3692940 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
3692875 TATTGTGCCT
3692885 AATCACGTTGAGTGTTTAAATATGATGG
1 AATCACGTTGAGTGTTTAAATATGATGG
3692913 AATCACGTTGAGTGTTTAAATATGATGG
1 AATCACGTTGAGTGTTTAAATATGATGG
3692941 TTATTTATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.07, G:0.25, T:0.36
Consensus pattern (28 bp):
AATCACGTTGAGTGTTTAAATATGATGG
Found at i:3696714 original size:117 final size:111
Alignment explanation
Indices: 3696300--3696761 Score: 620
Period size: 111 Copynumber: 4.1 Consensus size: 111
3696290 TCAAATTCAG
*
3696300 CAGCAGCAGCAGAATTTTCATGCGAATGGAACTGTATCTAACATGGGATCACCTCGATATGAGCA
1 CAGCAGCAGCAGAATTTTCATGCGAATGGAACTGTATCAAACATGGGATCACCTCGATATGAGCA
* * ** * *
3696365 GTCATATGTTCAAGGGATGGGTCATGCCTGGAATGGCCAGATGGCT
66 GTCATATGCTCAAGGCACAGGTCCTGCCTGGAATGGCCAGATGGTT
* *
3696411 CAGCAGCAGCAGAATTTTCATGCGAATGGAATTGTACCAAACATGGGATCACCTCGATATGAGCA
1 CAGCAGCAGCAGAATTTTCATGCGAATGGAACTGTATCAAACATGGGATCACCTCGATATGAGCA
* * *
3696476 CTCGTATGCTCAAGGGACAGGTCCTGCCTGGAATGGCCAGATGGTT
66 GTCATATGCTCAAGGCACAGGTCCTGCCTGGAATGGCCAGATGGTT
* * *
3696522 CAGCAGCAGCAGAATTTTCATGTGAACGGAACTGTATCGAACATGGGATCACCTCGATATGAGCA
1 CAGCAGCAGCAGAATTTTCATGCGAATGGAACTGTATCAAACATGGGATCACCTCGATATGAGCA
* * *
3696587 GACATATGCTCAAGGCACAGGTCCTGCCTGGAATGGTCAGCTGGTT
66 GTCATATGCTCAAGGCACAGGTCCTGCCTGGAATGGCCAGATGGTT
* * * * *
3696633 CAGCAGCATCATCAGAATAACTTTTATG-GAAATGGAAATGTATCAAACATGGGCTCGCCTCGAT
1 CAGCAG---CAGCAGAAT---TTTCATGCG-AATGGAACTGTATCAAACATGGGATCACCTCGAT
* *
3696697 ATGAGCAGTCATGTGCTCAAGGCACAGGTCCTGCCTGGAATGGCCAGCTGGTT
59 ATGAGCAGTCATATGCTCAAGGCACAGGTCCTGCCTGGAATGGCCAGATGGTT
*
3696750 CGGCAGCAGCAG
1 CAGCAGCAGCAG
3696762 GCCCACTTAC
Statistics
Matches: 311, Mismatches: 33, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
111 207 0.67
114 13 0.04
116 1 0.00
117 90 0.29
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (111 bp):
CAGCAGCAGCAGAATTTTCATGCGAATGGAACTGTATCAAACATGGGATCACCTCGATATGAGCA
GTCATATGCTCAAGGCACAGGTCCTGCCTGGAATGGCCAGATGGTT
Found at i:3698155 original size:17 final size:18
Alignment explanation
Indices: 3698129--3698166 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
3698119 AGTATGGCCC
*
3698129 AAAAAGAAAAGAAAA-GA
1 AAAAAAAAAAGAAAAGGA
3698146 AAAAAAAAAAGAAAAGGA
1 AAAAAAAAAAGAAAAGGA
3698164 AAA
1 AAA
3698167 CTAATAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAGAAAAGGA
Found at i:3706009 original size:21 final size:20
Alignment explanation
Indices: 3705967--3706011 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3705957 TCCAATCTAT
* **
3705967 TTTTTTCATTTTCCCTGTTA
1 TTTTTCCATTTTCCCAATTA
3705987 TTTTTCCATTTTCCCAATATA
1 TTTTTCCATTTTCCCAAT-TA
3706008 TTTT
1 TTTT
3706012 ATAATTGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.16, C:0.20, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTTTCCATTTTCCCAATTA
Found at i:3706191 original size:16 final size:16
Alignment explanation
Indices: 3706141--3706191 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 16
3706131 CTAAAAAAAG
3706141 TATA-TTATATAATTT
1 TATATTTATATAATTT
3706156 T-TATTTA-AT-A-TT
1 TATATTTATATAATTT
3706168 TATA-TTATATAATTT
1 TATATTTATATAATTT
*
3706183 TAAATTTAT
1 TATATTTAT
3706192 TATTGTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 11
0.71 0.02 0.27
Matches are distributed among these distances:
12 6 0.21
13 5 0.17
14 5 0.17
15 9 0.31
16 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TATATTTATATAATTT
Found at i:3720179 original size:16 final size:16
Alignment explanation
Indices: 3720158--3720225 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
3720148 TTTGGTTCGC
3720158 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
3720174 TGTATTGGATTGGAGG
1 TGTATTGGATTAGAGG
3720190 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
3720206 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
3720222 TGTA
1 TGTA
3720226 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.24, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:3720473 original size:18 final size:17
Alignment explanation
Indices: 3720452--3720486 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3720442 TTATTATTAA
*
3720452 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
3720470 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
3720487 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:3726128 original size:108 final size:110
Alignment explanation
Indices: 3725999--3726206 Score: 267
Period size: 110 Copynumber: 1.9 Consensus size: 110
3725989 GAAAAAACAA
* * *
3725999 TTTTTTGGGTGCTGGCTTGTCAATGGCCGGTACCCTGTAAACA-ATAAAAAAGAAAT-TTTTTTT
1 TTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTAAACAGATAAAAAAGAAATCTTTTTTT
*
3726062 TCATGTCAGAGTCAGATATAAAAATACGAAAAAAAATTTTAAATT
66 TCATGTCAGAATCAGATATAAAAATACGAAAAAAAATTTTAAATT
* * * *******
3726107 TTTTTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGTGAACAGTTAAATTTTTTTTCTTTTTTT
1 TTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTAAACAGATAAAAAAGAAATCTTTTTTT
*
3726172 TCGTGTCAGAATCAGATATAAAAATACGAAAAAAA
66 TCATGTCAGAATCAGATATAAAAATACGAAAAAAA
3726207 TAAATAATTT
Statistics
Matches: 83, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
108 38 0.46
109 5 0.06
110 40 0.48
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (110 bp):
TTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTAAACAGATAAAAAAGAAATCTTTTTTT
TCATGTCAGAATCAGATATAAAAATACGAAAAAAAATTTTAAATT
Found at i:3726228 original size:59 final size:59
Alignment explanation
Indices: 3726154--3726270 Score: 191
Period size: 59 Copynumber: 2.0 Consensus size: 59
3726144 TGAACAGTTA
*
3726154 AATTTTTTTTCTTTTTTTTCGTGTCAGAATCAGATATAAAAATACGAAAA-AAATAAAT
1 AATTTTTTTTCTTTTTTTTCGTATCAGAATCAGATATAAAAATACGAAAAGAAATAAAT
* *
3726212 AATTTTTTTCTTTTTTTTTTCGTATCAGAATCAGATATAAAAATATGAAAAGAAATAAA
1 AATTTTTTT-TCTTTTTTTTCGTATCAGAATCAGATATAAAAATACGAAAAGAAATAAA
3726271 AAAATTTATA
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
58 9 0.17
59 38 0.70
60 7 0.13
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.42
Consensus pattern (59 bp):
AATTTTTTTTCTTTTTTTTCGTATCAGAATCAGATATAAAAATACGAAAAGAAATAAAT
Found at i:3726680 original size:108 final size:107
Alignment explanation
Indices: 3726385--3726720 Score: 452
Period size: 107 Copynumber: 3.2 Consensus size: 107
3726375 GAAATAGAAA
* * * *
3726385 TTTTTATATTTTTTTCGTATTTTTATATCTGATTCTAACACG--AAAAAA-AATAATTTTTTTAC
1 TTTTTTTATTTTTTTCGTATTTTTATATCTGATTCTGACATGAAAAAAAAGAAAAATTTTTTTAC
*
3726447 TGTGTACTGGGTGCCGGTCATTGACAGGCCAGCACCC-AAAT
66 TGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAT
* * **
3726488 TTTTTTTATTTTTTTCTTATTTTTATATCTGATTCTGATATGAAAAAAAAG-AATTTTTTTTTAC
1 TTTTTTTATTTTTTTCGTATTTTTATATCTGATTCTGACATGAAAAAAAAGAAAAATTTTTTTAC
*
3726552 TGTGTACTGGGTGCCGGCCATTGACAGGCCAACACCCAAATAT
66 TGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAA-AT
* ***
3726595 TTTTTTTATTTTTTTCGTATTTTTATATCTTATTCTGACATGAAAAAAAAGAAAAAAAATTTTAC
1 TTTTTTTATTTTTTTCGTATTTTTATATCTGATTCTGACATGAAAAAAAAGAAAAATTTTTTTAC
* *
3726660 TGT-TCATTGGGTGCCGGCCATTCACAGGCCAGCACCCAAAAT
66 TGTGT-ACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAT
*
3726702 TTTTTTT-TCTTTTTCGTAT
1 TTTTTTTATTTTTTTCGTAT
3726721 ATCAGTATTA
Statistics
Matches: 204, Mismatches: 22, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
103 37 0.18
105 51 0.25
106 13 0.06
107 60 0.29
108 43 0.21
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (107 bp):
TTTTTTTATTTTTTTCGTATTTTTATATCTGATTCTGACATGAAAAAAAAGAAAAATTTTTTTAC
TGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAT
Found at i:3727659 original size:22 final size:22
Alignment explanation
Indices: 3727634--3727683 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
3727624 CCCCGTTCAA
3727634 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
** *
3727656 CTCATGTTTCACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
3727678 CTCATG
1 CTCATG
3727684 TTTGAACAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.32
Consensus pattern (22 bp):
CTCATGGCTAACGTACTAAGCT
Found at i:3727684 original size:22 final size:22
Alignment explanation
Indices: 3727644--3727686 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
3727634 CTCATGGCTA
3727644 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTC
3727666 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
3727687 GAACAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTC
Found at i:3745257 original size:16 final size:16
Alignment explanation
Indices: 3745215--3745258 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
3745205 TACTAAAAAT
3745215 TTATGAAAAAA-TATTG
1 TTAT-AAAAAATTATTG
3745231 TTATAAAAAATTATT-
1 TTATAAAAAATTATTG
3745246 TTAATAAAAAATT
1 TT-ATAAAAAATT
3745259 TATGTATTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.31
16 18 0.69
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (16 bp):
TTATAAAAAATTATTG
Found at i:3756662 original size:60 final size:60
Alignment explanation
Indices: 3756569--3756789 Score: 365
Period size: 60 Copynumber: 3.7 Consensus size: 60
3756559 AGGAAAAGGG
3756569 AAGCCAGGGGGTGGCACTCATGTGAACGTTGG-GCGCAAAGGAGTTGGAGTGAACACAGGA
1 AAGCCAGGGGGTGGCACTCATGTGAACGTTGGAG-GCAAAGGAGTTGGAGTGAACACAGGA
3756629 AAGCCAGGGGGTGGCACTCATGTGAACGTTGG-GCGCAAAGGAGTTGGAGTGAACACAGGA
1 AAGCCAGGGGGTGGCACTCATGTGAACGTTGGAG-GCAAAGGAGTTGGAGTGAACACAGGA
* * *
3756689 AAGCCAGGGGGTGGCACTCATGTGAATGTTGGAGGCAAAGGAGTTGGGGTGAACACTGGA
1 AAGCCAGGGGGTGGCACTCATGTGAACGTTGGAGGCAAAGGAGTTGGAGTGAACACAGGA
* *
3756749 AAGCCAGGAGGTGGCACCCATGTGAACGTTGGAGGCAAAGG
1 AAGCCAGGGGGTGGCACTCATGTGAACGTTGGAGGCAAAGG
3756790 TGGAGGAGTA
Statistics
Matches: 154, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
60 153 0.99
61 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.40, T:0.15
Consensus pattern (60 bp):
AAGCCAGGGGGTGGCACTCATGTGAACGTTGGAGGCAAAGGAGTTGGAGTGAACACAGGA
Found at i:3763125 original size:42 final size:42
Alignment explanation
Indices: 3763073--3763180 Score: 126
Period size: 42 Copynumber: 2.6 Consensus size: 42
3763063 GAGTACATCG
* *
3763073 TAAACAGAAACCCATAAGGGTTCATCTAAAGCTCAAAAGAGC
1 TAAACAGAAACCCATAAGGGTTAAACTAAAGCTCAAAAGAGC
* * *
3763115 TAAACGGAAACCCATTAGGGTTAAACTGAAGCTCAAAAGAGC
1 TAAACAGAAACCCATAAGGGTTAAACTAAAGCTCAAAAGAGC
* * * * *
3763157 TGAACTGAAATCCAGAAGCGTTAA
1 TAAACAGAAACCCATAAGGGTTAA
3763181 TTTGAAACTC
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.18
Consensus pattern (42 bp):
TAAACAGAAACCCATAAGGGTTAAACTAAAGCTCAAAAGAGC
Found at i:3773551 original size:53 final size:53
Alignment explanation
Indices: 3773488--3773595 Score: 207
Period size: 53 Copynumber: 2.0 Consensus size: 53
3773478 TAGTACAACA
*
3773488 ACGGAAAACGAAAGCGAGTCAAAGTTGCGACTGTAACAAAAATGATAGCAAAG
1 ACGGAAAACGAAAACGAGTCAAAGTTGCGACTGTAACAAAAATGATAGCAAAG
3773541 ACGGAAAACGAAAACGAGTCAAAGTTGCGACTGTAACAAAAATGATAGCAAAG
1 ACGGAAAACGAAAACGAGTCAAAGTTGCGACTGTAACAAAAATGATAGCAAAG
3773594 AC
1 AC
3773596 AGAACAGGGA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (53 bp):
ACGGAAAACGAAAACGAGTCAAAGTTGCGACTGTAACAAAAATGATAGCAAAG
Found at i:3773592 original size:29 final size:29
Alignment explanation
Indices: 3773507--3773593 Score: 78
Period size: 29 Copynumber: 3.2 Consensus size: 29
3773497 GAAAGCGAGT
3773507 CAAAGTTGCGACTGTAACAAAAATGATAG
1 CAAAGTTGCGACTGTAACAAAAATGATAG
** * * *
3773536 CAAAGACG-GA---AAACGAAAACG--AG
1 CAAAGTTGCGACTGTAACAAAAATGATAG
3773559 TCAAAGTTGCGACTGTAACAAAAATGATAG
1 -CAAAGTTGCGACTGTAACAAAAATGATAG
3773589 CAAAG
1 CAAAG
3773594 ACAGAACAGG
Statistics
Matches: 41, Mismatches: 10, Indels: 14
0.63 0.15 0.22
Matches are distributed among these distances:
23 2 0.05
24 6 0.15
25 10 0.24
28 10 0.24
29 11 0.27
30 2 0.05
ACGTcount: A:0.48, C:0.15, G:0.22, T:0.15
Consensus pattern (29 bp):
CAAAGTTGCGACTGTAACAAAAATGATAG
Found at i:3774766 original size:35 final size:36
Alignment explanation
Indices: 3774685--3774775 Score: 98
Period size: 35 Copynumber: 2.6 Consensus size: 36
3774675 CGGAATAAGT
* * *
3774685 GTATATATATTAAAAATATTTAAATTTAAAATATATA
1 GTATATATATT-ATAATATTAAAACTTAAAATATATA
*
3774722 TTATA-ATATTATAATATTAAAACTTAAAAGT-TA-A
1 GTATATATATTATAATATTAAAACTTAAAA-TATATA
*
3774756 GTATATATATTATTATATTA
1 GTATATATATTATAATATTA
3774776 TAATGATAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
34 5 0.11
35 31 0.67
36 6 0.13
37 4 0.09
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (36 bp):
GTATATATATTATAATATTAAAACTTAAAATATATA
Found at i:3774792 original size:6 final size:6
Alignment explanation
Indices: 3774783--3774866 Score: 55
Period size: 6 Copynumber: 14.0 Consensus size: 6
3774773 TTATAATGAT
* ** * *
3774783 AAAGAA AAAGAA AAAGAA ATAGAA AAAGAA GGAGAG AAAG-A AACGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* * * *
3774830 ATAGAG AAGGAA AGAAAAA AAAGAA AAA-AA GAAAGAA
1 AAAGAA AAAGAA A-AAGAA AAAGAA AAAGAA -AAAGAA
3774867 GGAAGGAGAA
Statistics
Matches: 56, Mismatches: 18, Indels: 7
0.69 0.22 0.09
Matches are distributed among these distances:
5 5 0.09
6 45 0.80
7 6 0.11
ACGTcount: A:0.74, C:0.01, G:0.23, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:3776053 original size:20 final size:20
Alignment explanation
Indices: 3776028--3776067 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3776018 TTGAATATGG
3776028 TATGGATAAAACAATTGCAT
1 TATGGATAAAACAATTGCAT
*
3776048 TATGGATAAAGCAATTGCAT
1 TATGGATAAAACAATTGCAT
3776068 AAATGAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.30
Consensus pattern (20 bp):
TATGGATAAAACAATTGCAT
Found at i:3777761 original size:20 final size:19
Alignment explanation
Indices: 3777736--3777782 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
3777726 TTTAAAGTTT
*
3777736 AAATTTTATTAAAAATCATA
1 AAATTTTATGAAAAAT-ATA
* *
3777756 AAATTTTATGAAAACTTTA
1 AAATTTTATGAAAAATATA
3777775 AAATTTTA
1 AAATTTTA
3777783 AGTTTGTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (19 bp):
AAATTTTATGAAAAATATA
Found at i:3777769 original size:19 final size:20
Alignment explanation
Indices: 3777736--3777782 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
3777726 TTTAAAGTTT
3777736 AAATTTTATTAAAAA-TCATA
1 AAATTTTATTAAAAACT-ATA
* *
3777756 AAATTTTA-TGAAAACTTTA
1 AAATTTTATTAAAAACTATA
3777775 AAATTTTA
1 AAATTTTA
3777783 AGTTTGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (20 bp):
AAATTTTATTAAAAACTATA
Found at i:3777911 original size:17 final size:18
Alignment explanation
Indices: 3777891--3777926 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
3777881 GTTATTTTAA
3777891 TAAAATGTTTATAT-TTT
1 TAAAATGTTTATATCTTT
*
3777908 TAAAATTTTTATATCTTT
1 TAAAATGTTTATATCTTT
3777926 T
1 T
3777927 GTTTATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (18 bp):
TAAAATGTTTATATCTTT
Found at i:3779122 original size:19 final size:19
Alignment explanation
Indices: 3779098--3779134 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3779088 AAAAAAAATT
3779098 ATTTTAATATAATATTAAC
1 ATTTTAATATAATATTAAC
3779117 ATTTTAATATAATATTAA
1 ATTTTAATATAATATTAA
3779135 TATTGACATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTTAATATAATATTAAC
Found at i:3788299 original size:3 final size:3
Alignment explanation
Indices: 3788291--3788335 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
3788281 CCTCGCTATT
* * *
3788291 GAA GAA GAA GAG GAG GAG GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
3788336 CATCACGAGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:3793696 original size:5 final size:5
Alignment explanation
Indices: 3793686--3793712 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
3793676 TCGAGGCCCG
3793686 TCCCA TCCCA TCCCA TCCCA TCCCA TC
1 TCCCA TCCCA TCCCA TCCCA TCCCA TC
3793713 AGTTGTGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.59, G:0.00, T:0.22
Consensus pattern (5 bp):
TCCCA
Found at i:3797706 original size:19 final size:20
Alignment explanation
Indices: 3797674--3797713 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
3797664 AAAGTAAAAT
* *
3797674 AATATTATTTAAAT-TATTA
1 AATATAATTAAAATGTATTA
3797693 AATATAATTAAAATGTATTA
1 AATATAATTAAAATGTATTA
3797713 A
1 A
3797714 CTTACAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
AATATAATTAAAATGTATTA
Found at i:3803919 original size:122 final size:123
Alignment explanation
Indices: 3803764--3804003 Score: 383
Period size: 122 Copynumber: 2.0 Consensus size: 123
3803754 TCAATAGCAC
*
3803764 GATCATATTCATCTGCATGATTATAAACCCATCATAAGTCAATCAATGTGCATTTAAT-AAAAAA
1 GATCATATTCATCCGCATGATTATAAACCCATCATAAGTCAATCAATGTGCATTTAATAAAAAAA
* *
3803828 CAAATGCTAAAGTTTAACTAGACTAAGAGCAAAAGCCGAGTAGATCAATACTATTGAT
66 CAAATGCTAAAGTTTAACTAGACTAAGAGCAAAAGCCGAGCAGATCAAAACTATTGAT
* * *
3803886 GATCATATTCATCCGCATGATTGTAAACTCATCATAAGTCGATCAATGTGCATTTAATAAAAAAA
1 GATCATATTCATCCGCATGATTATAAACCCATCATAAGTCAATCAATGTGCATTTAATAAAAAAA
* * * *
3803951 CAAATGCTACAGTTTTACTAGACTACGAGCAAAAGCTGAGCAGATCAAAACTA
66 CAAATGCTAAAGTTTAACTAGACTAAGAGCAAAAGCCGAGCAGATCAAAACTA
3804004 AGATTCAACT
Statistics
Matches: 107, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
122 54 0.50
123 53 0.50
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (123 bp):
GATCATATTCATCCGCATGATTATAAACCCATCATAAGTCAATCAATGTGCATTTAATAAAAAAA
CAAATGCTAAAGTTTAACTAGACTAAGAGCAAAAGCCGAGCAGATCAAAACTATTGAT
Found at i:3812766 original size:94 final size:92
Alignment explanation
Indices: 3812573--3812766 Score: 219
Period size: 94 Copynumber: 2.1 Consensus size: 92
3812563 TTAATACTTT
* * * * * * *
3812573 TACTTTTTGGAGCATCTTTTTTCTTTTTTTTTTTGGATAATTATACTGTTTGAAAAATCAATCTA
1 TACTTTTTGAAACACCTTTCTTCTTTTTTCTTTTGGATAATTACACTGTTTGAAAAAACAATCTA
* * *
3812638 CAATACCACGTAAGTTCTTCTGAATTG
66 CAATACCACGCAACTTCTTCAGAATTG
*
3812665 TAATTTTTGAAACACCTTTCTTCTTCTTCTTCTTTTGGATAATTACACT-TTTAGAAAAAACAAT
1 TACTTTTTGAAACACCTTTCTTCTT-TT-TTCTTTTGGATAATTACACTGTTT-GAAAAAACAAT
* * * *
3812729 CTATAATACCATGCAACTTTTTCAGGATTG
63 CTACAATACCACGCAACTTCTTCAGAATTG
3812759 TACTTTTT
1 TACTTTTT
3812767 TGAACATCAA
Statistics
Matches: 83, Mismatches: 16, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
92 20 0.24
93 5 0.06
94 58 0.70
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.46
Consensus pattern (92 bp):
TACTTTTTGAAACACCTTTCTTCTTTTTTCTTTTGGATAATTACACTGTTTGAAAAAACAATCTA
CAATACCACGCAACTTCTTCAGAATTG
Found at i:3816127 original size:20 final size:21
Alignment explanation
Indices: 3816090--3816132 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3816080 ATATAAGCAA
*
3816090 AAAAAAAAAAGTTCAAAGGAG
1 AAAAAAAAAAGTTCAAAGAAG
*
3816111 AAAAAAAAAAG-TGAAAGAAG
1 AAAAAAAAAAGTTCAAAGAAG
3816131 AA
1 AA
3816133 TCAAAAGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.72, C:0.02, G:0.19, T:0.07
Consensus pattern (21 bp):
AAAAAAAAAAGTTCAAAGAAG
Found at i:3830495 original size:20 final size:20
Alignment explanation
Indices: 3830455--3830495 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3830445 AAATATTGTT
* * *
3830455 AAAATATATTTAATAGTTTA
1 AAAACATATTTAAAAGCTTA
3830475 AAAACATATTTAAAAGCTTA
1 AAAACATATTTAAAAGCTTA
3830495 A
1 A
3830496 GATATTGTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.37
Consensus pattern (20 bp):
AAAACATATTTAAAAGCTTA
Found at i:3833316 original size:46 final size:46
Alignment explanation
Indices: 3833249--3833378 Score: 208
Period size: 46 Copynumber: 2.8 Consensus size: 46
3833239 AGTGTGGAAC
*
3833249 GTAGGTATGGTATTTCAGTAAAGAAAATCATACTGAGTTGTGAA-AA
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGT-AAGAA
3833295 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTAAGAA
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTAAGAA
* * *
3833341 GTAGGTATGATATTTCAATAACGAAAACCATACTGAGT
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGT
3833379 GTTGACACCA
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
45 2 0.03
46 77 0.97
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.29
Consensus pattern (46 bp):
GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTAAGAA
Found at i:3834668 original size:2 final size:2
Alignment explanation
Indices: 3834661--3834691 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3834651 AGCATAATGC
*
3834661 AT AT AT AT AG AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3834692 GAATAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3834771 original size:3 final size:3
Alignment explanation
Indices: 3834757--3834852 Score: 81
Period size: 3 Copynumber: 32.0 Consensus size: 3
3834747 CAAATAAAAC
* * *
3834757 TAA TAA TGA TAA TAA TTAA TAA TAA TAA TAT TAA TAA TCA TAA TAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
3834803 TAA AAGA TAA TAA CAT TAA -AA TAA TGAA GAA -AA -AA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
3834847 TAA TAA
1 TAA TAA
3834853 AAGTGCTAAA
Statistics
Matches: 75, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
2 6 0.08
3 62 0.83
4 7 0.09
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:3834792 original size:31 final size:30
Alignment explanation
Indices: 3834757--3834851 Score: 91
Period size: 31 Copynumber: 3.0 Consensus size: 30
3834747 CAAATAAAAC
3834757 TAATAATGATAATAATTAATAATAATAATAT
1 TAATAATGATAATAA-TAATAATAATAATAT
* * *
3834788 TAATAATCATAATAATAAAAGATAATAACAT
1 TAATAATGATAATAATAATA-ATAATAATAT
* *
3834819 TAAAATAATGAAGAAAAAATAATAATAATAATA
1 T--AATAATG-A-TAATAATAATAATAATAATA
3834852 AAAGTGCTAA
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
30 4 0.08
31 24 0.47
33 6 0.12
34 9 0.18
35 8 0.16
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (30 bp):
TAATAATGATAATAATAATAATAATAATAT
Found at i:3839174 original size:12 final size:12
Alignment explanation
Indices: 3839157--3839181 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3839147 CAGCAGAAAG
3839157 GAGTGAAGAGAA
1 GAGTGAAGAGAA
3839169 GAGTGAAGAGAA
1 GAGTGAAGAGAA
3839181 G
1 G
3839182 GCATTTCAAG
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:0.48, C:0.00, G:0.44, T:0.08
Consensus pattern (12 bp):
GAGTGAAGAGAA
Found at i:3844407 original size:29 final size:30
Alignment explanation
Indices: 3844349--3844422 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 30
3844339 ATTAATAATT
* * *
3844349 TATAAGAATTAGATTAAATCAAAATTTTATG
1 TATAA-AATTACATAAAATCAAAATTTTATA
*
3844380 TATAAAATTACATAAAATTAAAA-TTTATA
1 TATAAAATTACATAAAATCAAAATTTTATA
*
3844409 TATACAATTACATA
1 TATAAAATTACATA
3844423 TTAAATTATA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 18 0.47
30 15 0.39
31 5 0.13
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.38
Consensus pattern (30 bp):
TATAAAATTACATAAAATCAAAATTTTATA
Found at i:3856092 original size:22 final size:22
Alignment explanation
Indices: 3856064--3856165 Score: 132
Period size: 22 Copynumber: 4.6 Consensus size: 22
3856054 TTTATTGTTC
*
3856064 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
3856086 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
3856108 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
3856130 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
3856152 AAACATGAGAGCTT
1 AAACATGAGAGCTT
3856166 TCATTCAAAC
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 70 1.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:3865259 original size:2 final size:2
Alignment explanation
Indices: 3865209--3865241 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
3865199 GTAAATTTGT
3865209 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3865242 TAAAGTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.