Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 36 of 320
Found at i:10247458 original size:16 final size:16
Alignment explanation
Indices: 10247427--10247463 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
10247417 ACATGAATAA
10247427 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
10247443 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
10247459 TATTA
1 TATTA
10247464 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:10247515 original size:22 final size:22
Alignment explanation
Indices: 10247475--10247530 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
10247465 AATAAAATTG
*
10247475 AAATATTAAA-TA-ATTTATTA
1 AAATAATAAATTATATTTATTA
10247495 AAATAATAAATTATATTTATTA
1 AAATAATAAATTATATTTATTA
* * *
10247517 TATTAATAATTTAT
1 AAATAATAAATTAT
10247531 TATAAGACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 9 0.30
21 2 0.07
22 19 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATAATAAATTATATTTATTA
Found at i:10251701 original size:26 final size:21
Alignment explanation
Indices: 10251649--10251690 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
10251639 TTGAATTTGT
10251649 TATTATTATTAATTAATTTCA
1 TATTATTATTAATTAATTTCA
*
10251670 AATTATATGATTAATTAATTT
1 TATTAT-T-ATTAATTAATTT
10251691 TTACATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 1 0.06
23 12 0.67
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (21 bp):
TATTATTATTAATTAATTTCA
Found at i:10255316 original size:29 final size:29
Alignment explanation
Indices: 10255270--10255330 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
10255260 ACAATTATGT
10255270 TACTACATTTACACCTGAACTTACCTCGG
1 TACTACATTTACACCTGAACTTACCTCGG
*
10255299 TACTACATTTACATCTGAACTTACCTCGG
1 TACTACATTTACACCTGAACTTACCTCGG
10255328 TAC
1 TAC
10255331 AAAATAAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.33
Consensus pattern (29 bp):
TACTACATTTACACCTGAACTTACCTCGG
Found at i:10257880 original size:39 final size:39
Alignment explanation
Indices: 10257836--10257963 Score: 202
Period size: 39 Copynumber: 3.3 Consensus size: 39
10257826 TATGAGATTG
10257836 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
1 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
*
10257875 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTAGA
1 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
* * * **
10257914 AATATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGA
1 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
10257953 AAAATATCCGG
1 AAAATATCCGG
10257964 GTTAAAGACC
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 81 1.00
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (39 bp):
AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
Found at i:10257977 original size:78 final size:76
Alignment explanation
Indices: 10257835--10257989 Score: 186
Period size: 78 Copynumber: 2.0 Consensus size: 76
10257825 GTATGAGATT
* * * **
10257835 GAAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGAAAAATATCCGGACATGAGGTCCGCA
1 GAAAATATCCGGACATAAGGTCCGCAGGCTACATGCTGGAAAAATATCCGGACATAAGACCCGCA
*
10257900 GGCTATATGCTA
66 GGCT-TACGCTA
* * **
10257912 GAAATATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAAAATATCCGG-GTTAAAGACCCG
1 GAAA-ATATCCGGACATAAGGTCCGCAGGCTACATGCTGGAAAAATATCCGGACAT-AAGACCCG
10257976 CAGGCTTACGCTA
64 CAGGCTTACGCTA
10257989 G
1 G
10257990 TGATATATTC
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
77 12 0.18
78 54 0.82
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (76 bp):
GAAAATATCCGGACATAAGGTCCGCAGGCTACATGCTGGAAAAATATCCGGACATAAGACCCGCA
GGCTTACGCTA
Found at i:10261226 original size:29 final size:30
Alignment explanation
Indices: 10261167--10261224 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
10261157 TCCGAGCCTT
*
10261167 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
10261197 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
10261225 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:10261455 original size:13 final size:13
Alignment explanation
Indices: 10261437--10261467 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
10261427 TTCCAGCAAC
10261437 TATGAATTTATTT
1 TATGAATTTATTT
10261450 TATGAATTTATTT
1 TATGAATTTATTT
*
10261463 GATGA
1 TATGA
10261468 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:10261637 original size:50 final size:50
Alignment explanation
Indices: 10261562--10261754 Score: 296
Period size: 50 Copynumber: 3.8 Consensus size: 50
10261552 ATTTGGGTAA
10261562 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
10261612 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * *
10261662 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
10261712 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
10261755 TGTTATTATC
Statistics
Matches: 129, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 95 0.74
51 34 0.26
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:10265375 original size:28 final size:28
Alignment explanation
Indices: 10265322--10265376 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
10265312 CTTAAAGAGG
* *
10265322 TAAAGCCACTTTAAAGAAGTGTGTTATT
1 TAAAGCCACTTTAAAGAAATGAGTTATT
*
10265350 TAAATCCACTTTAATA-AAATGAGTTAT
1 TAAAGCCACTTTAA-AGAAATGAGTTAT
10265377 CTTTAAAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 22 0.96
29 1 0.04
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (28 bp):
TAAAGCCACTTTAAAGAAATGAGTTATT
Found at i:10267220 original size:18 final size:17
Alignment explanation
Indices: 10267179--10267223 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
10267169 TGTTTTAACG
*
10267179 AATTTAATATTATATTT
1 AATTTAATATTATATCT
10267196 AATTTAATATT-TATCT
1 AATTTAATATTATATCT
10267212 ATATATTAATAT
1 A-AT-TTAATAT
10267224 GAGATATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 5 0.20
17 13 0.52
18 7 0.28
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
AATTTAATATTATATCT
Found at i:10278904 original size:15 final size:16
Alignment explanation
Indices: 10278878--10278914 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
10278868 CCTTTTTTTT
10278878 TCTTTTGTTTTCAT-TC
1 TCTTTTGTTTTC-TCTC
10278894 TCTTTTG-TTTCTCTC
1 TCTTTTGTTTTCTCTC
10278909 TCTTTT
1 TCTTTT
10278915 TTCCTCCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 1 0.05
15 12 0.60
16 7 0.35
ACGTcount: A:0.03, C:0.22, G:0.05, T:0.70
Consensus pattern (16 bp):
TCTTTTGTTTTCTCTC
Found at i:10279137 original size:23 final size:23
Alignment explanation
Indices: 10279111--10279156 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
10279101 AGAAGACAAT
10279111 AGAAAATAAAGA-AAAAAATTAAA
1 AGAAAATAAA-ATAAAAAATTAAA
*
10279134 AGAACATAAAATAAAAAATTAAA
1 AGAAAATAAAATAAAAAATTAAA
10279157 TTGCTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 1 0.05
23 20 0.95
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (23 bp):
AGAAAATAAAATAAAAAATTAAA
Found at i:10280061 original size:24 final size:24
Alignment explanation
Indices: 10280041--10280085 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
10280031 AATAAAAGTT
10280041 TTATATTAATATTAAACAAAAAAA
1 TTATATTAATATTAAACAAAAAAA
*
10280065 TTATATTAATA-TAAACTAAAA
1 TTATATTAATATTAAACAAAAA
10280086 TAAAATCCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (24 bp):
TTATATTAATATTAAACAAAAAAA
Found at i:10289491 original size:35 final size:36
Alignment explanation
Indices: 10289394--10289484 Score: 123
Period size: 35 Copynumber: 2.6 Consensus size: 36
10289384 ATTTTCTATT
* *
10289394 TTGGTGTATTTCGGTTGGA-CTAGCTCTTATGAGCA
1 TTGGTGTGTTTCGGATGGATCTAGCTCTTATGAGCA
* * *
10289429 TTGGTATGTTTCAGAGGGAT-TAGCTCTTATGAGCA
1 TTGGTGTGTTTCGGATGGATCTAGCTCTTATGAGCA
10289464 TTGGTGTGTTTCGGATGGATC
1 TTGGTGTGTTTCGGATGGATC
10289485 GACTCTTGTG
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.18, C:0.12, G:0.31, T:0.40
Consensus pattern (36 bp):
TTGGTGTGTTTCGGATGGATCTAGCTCTTATGAGCA
Found at i:10291273 original size:19 final size:20
Alignment explanation
Indices: 10291249--10291297 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
10291239 GGATTTTATT
*
10291249 TTATTTTATTTTCATAT-AA
1 TTATTTTATTTTAATATAAA
* *
10291268 TTATTTAATATTAATATAAA
1 TTATTTTATTTTAATATAAA
10291288 TT-TTTTATTT
1 TTATTTTATTT
10291298 AATTTTTATA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
TTATTTTATTTTAATATAAA
Found at i:10291313 original size:24 final size:25
Alignment explanation
Indices: 10291268--10291331 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 25
10291258 TTTCATATAA
* * *
10291268 TTATTTAATATTAAT-ATAAATTTT
1 TTATTTAATTTTTATAATAAATTAT
10291292 TTATTTAATTTTTATAAT-AATTAT
1 TTATTTAATTTTTATAATAAATTAT
*
10291316 TTA--TAATTTATATAAT
1 TTATTTAATTTTTATAAT
10291332 TCATTTTACT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
22 12 0.34
24 21 0.60
25 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TTATTTAATTTTTATAATAAATTAT
Found at i:10299813 original size:9 final size:9
Alignment explanation
Indices: 10299801--10299830 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
10299791 TTGAATTAAA
10299801 TTATTCGAG
1 TTATTCGAG
*
10299810 TTATTCGAA
1 TTATTCGAG
10299819 TTATTCGAG
1 TTATTCGAG
10299828 TTA
1 TTA
10299831 CTCAAATAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.47
Consensus pattern (9 bp):
TTATTCGAG
Found at i:10299897 original size:23 final size:24
Alignment explanation
Indices: 10299845--10299897 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
10299835 AATAAGAAAT
*
10299845 TTCGAATTTCAAATTCAAGTTAAA
1 TTCGAATTTCAAATTCAAGATAAA
*
10299869 TT-GAATTTTACAATTCAA-AT-AA
1 TTCGAATTTCA-AATTCAAGATAAA
10299891 TTCGAAT
1 TTCGAAT
10299898 AACATATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 4 0.16
23 12 0.48
24 9 0.36
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.40
Consensus pattern (24 bp):
TTCGAATTTCAAATTCAAGATAAA
Found at i:10300000 original size:19 final size:19
Alignment explanation
Indices: 10299976--10300039 Score: 85
Period size: 20 Copynumber: 3.4 Consensus size: 19
10299966 CAAAAATTAA
*
10299976 AAAAATCAAAATAATTTTT
1 AAAAATTAAAATAATTTTT
10299995 AAAAATTTAAAATAATTTTT
1 AAAAA-TTAAAATAATTTTT
* *
10300015 AAAATTTAAAAT-ATTTAT
1 AAAAATTAAAATAATTTTT
10300033 AAAAATT
1 AAAAATT
10300040 CTAAATTTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
18 11 0.28
19 12 0.30
20 17 0.43
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAAATTAAAATAATTTTT
Found at i:10300006 original size:20 final size:20
Alignment explanation
Indices: 10299983--10300044 Score: 92
Period size: 19 Copynumber: 3.1 Consensus size: 20
10299973 TAAAAAAATC
10299983 AAAATAATTTTTAAAAATTT
1 AAAATAATTTTTAAAAATTT
10300003 AAAATAATTTTT-AAAATTT
1 AAAATAATTTTTAAAAATTT
*
10300022 AAAAT-ATTTATAAAAATTCT
1 AAAATAATTTTTAAAAATT-T
10300042 AAA
1 AAA
10300045 TTTTGTATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
18 5 0.13
19 18 0.46
20 16 0.41
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAATAATTTTTAAAAATTT
Found at i:10300449 original size:21 final size:21
Alignment explanation
Indices: 10300423--10300462 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
10300413 ACCTTATCTA
10300423 AAGTTAAAA-GTCAAAACTATC
1 AAGTTAAAAGGT-AAAACTATC
10300444 AAGTTAAAAGGTAAAACTA
1 AAGTTAAAAGGTAAAACTA
10300463 CGTTGTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.23
Consensus pattern (21 bp):
AAGTTAAAAGGTAAAACTATC
Found at i:10300889 original size:3 final size:3
Alignment explanation
Indices: 10300871--10300909 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
10300861 TGTGTTATTT
*
10300871 TTC TCTC TTT TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC T-TC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
10300910 TTTTTTTCAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:10305523 original size:37 final size:37
Alignment explanation
Indices: 10305470--10305572 Score: 179
Period size: 37 Copynumber: 2.8 Consensus size: 37
10305460 CGAATAGTCG
* *
10305470 CCACAGGTAGTTATCGGGTCTTACCCGGACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
*
10305507 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
10305544 CCACACGTAGTCATCGGGTCTTACCCGGA
1 CCACACGTAGTCATCGGGTCTTACCCGGA
10305573 ATACATTTCC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 63 1.00
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.23
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
Found at i:10305799 original size:48 final size:48
Alignment explanation
Indices: 10305745--10306149 Score: 711
Period size: 48 Copynumber: 8.4 Consensus size: 48
10305735 GCCGAATCAC
*
10305745 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCGCAT
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
* * *
10305793 TAGCCATTTGGCTTTACCACGTATACATATCTCATACATATTTCACAC
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
* * *
10305841 TAGCCATTCGGCTTTACCACGTATACATATCTCATACATAGTTCACAC
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
10305889 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
* *
10305937 TTGCTATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
10305985 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
*
10306033 TTGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
*
10306081 TAGCCATTCGGCTTTACCACATATACATGTCTCATACATATTTCACAT
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
10306129 TAGCCATTCGGCTTTACCACA
1 TAGCCATTCGGCTTTACCACA
10306150 CACATATATA
Statistics
Matches: 341, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 341 1.00
ACGTcount: A:0.29, C:0.27, G:0.08, T:0.35
Consensus pattern (48 bp):
TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
Found at i:10310083 original size:26 final size:26
Alignment explanation
Indices: 10310053--10310102 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
10310043 CCACTTAATC
*
10310053 GGGGAATCAGCACTTAGCAACCCCTT
1 GGGGAATCAGCACATAGCAACCCCTT
10310079 GGGGAATCAGCACATAGCAACCCC
1 GGGGAATCAGCACATAGCAACCCC
10310103 CTTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.32, G:0.24, T:0.14
Consensus pattern (26 bp):
GGGGAATCAGCACATAGCAACCCCTT
Found at i:10310249 original size:104 final size:102
Alignment explanation
Indices: 10310021--10310283 Score: 393
Period size: 104 Copynumber: 2.6 Consensus size: 102
10310011 ACCGTTATTA
* * * *
10310021 GTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGAAT
1 GTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTGGGGGAAT
** *
10310086 CAGCACATAGCAACCCCCTTTTTATTTCAGAGATACG
66 CAGCACATAGCAACCCCCTTTACATTTCAAAGATACG
10310123 GTGGATATCGCACTTAGCACCACCAATGAA-CTGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
1 GTGGATATCGCACTTAGCACCACCAATGAATC-GGGGAATCAGCACTTAGCAACCCCT-GGGGGA
10310187 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACG
64 ATCAGCACATAGCAACCCCCTTT-ACATTTCAAAGATACG
* * **
10310227 GTGGATATCGCACATGGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
10310284 TTATGTACAA
Statistics
Matches: 146, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
101 1 0.01
102 52 0.36
103 28 0.19
104 64 0.44
105 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.20
Consensus pattern (102 bp):
GTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTGGGGGAAT
CAGCACATAGCAACCCCCTTTACATTTCAAAGATACG
Found at i:10312438 original size:28 final size:28
Alignment explanation
Indices: 10312396--10312464 Score: 111
Period size: 28 Copynumber: 2.5 Consensus size: 28
10312386 GACTGATTTC
*
10312396 GCACACATAGCGCTCGATTGAAGAACTT
1 GCACACATAGTGCTCGATTGAAGAACTT
*
10312424 GTACACATAGTGCTCGATTGAAGAACTT
1 GCACACATAGTGCTCGATTGAAGAACTT
*
10312452 GCACACACAGTGC
1 GCACACATAGTGC
10312465 CTCATAATTC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.22
Consensus pattern (28 bp):
GCACACATAGTGCTCGATTGAAGAACTT
Found at i:10312540 original size:40 final size:40
Alignment explanation
Indices: 10312476--10312630 Score: 260
Period size: 40 Copynumber: 3.9 Consensus size: 40
10312466 TCATAATTCC
* *
10312476 AGCACGAATGC-CTTCGAGG-TTTAGCCCGGATATATTACT
1 AGCACGAATGCTCTTCG-GGACTTAGCCCGGATATATCACT
*
10312515 AGCACGAATACTCTTCGGGACTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
10312555 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
10312595 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATAT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATAT
10312631 AACTCTCAAT
Statistics
Matches: 110, Mismatches: 4, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
39 12 0.11
40 98 0.89
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
Found at i:10314198 original size:48 final size:48
Alignment explanation
Indices: 10314144--10314548 Score: 720
Period size: 48 Copynumber: 8.4 Consensus size: 48
10314134 GCCGAATCAC
*
10314144 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCGCAT
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
*
10314192 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAC
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
* *
10314240 TAGCCATTCGGCTTTACCACCTATACATATCTCATACATATTTCACAG
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
**
10314288 TAGCCATTCGGCTTTATTACATATACATATCTCATACATATTTCACAT
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
*
10314336 TTGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
*
10314384 TTGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
*
10314432 TTGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
*
10314480 TAGCCAGTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
10314528 TAGCCATTCGGCTTTACCACA
1 TAGCCATTCGGCTTTACCACA
10314549 CACATATATA
Statistics
Matches: 343, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 343 1.00
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (48 bp):
TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
Found at i:10319385 original size:12 final size:12
Alignment explanation
Indices: 10319368--10319402 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
10319358 TGAGACAAGA
10319368 TATTCTTTAAAT
1 TATTCTTTAAAT
10319380 TATTCTTTTAAAT
1 TATTC-TTTAAAT
*
10319393 TATTTTTTAA
1 TATTCTTTAA
10319403 GTAACATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (12 bp):
TATTCTTTAAAT
Found at i:10319391 original size:13 final size:13
Alignment explanation
Indices: 10319368--10319402 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
10319358 TGAGACAAGA
10319368 TATTC-TTTAAAT
1 TATTCTTTTAAAT
10319380 TATTCTTTTAAAT
1 TATTCTTTTAAAT
10319393 TATT-TTTTAA
1 TATTCTTTTAA
10319403 GTAACATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (13 bp):
TATTCTTTTAAAT
Found at i:10319615 original size:21 final size:21
Alignment explanation
Indices: 10319565--10319609 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
10319555 ATATTAAGAA
*
10319565 TATTATTAAATTATATATTAT
1 TATTGTTAAATTATATATTAT
*
10319586 TATTGTTAAATTATGTATTAT
1 TATTGTTAAATTATATATTAT
10319607 TAT
1 TAT
10319610 ATTTAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (21 bp):
TATTGTTAAATTATATATTAT
Found at i:10319825 original size:16 final size:16
Alignment explanation
Indices: 10319802--10319847 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
10319792 CTACTACAGT
*
10319802 TCTATTCTATTATAAC
1 TCTATTCTATTACAAC
*
10319818 TTTATTCTATTACAAC
1 TCTATTCTATTACAAC
*
10319834 TCTATTCCATTACA
1 TCTATTCTATTACA
10319848 CTGAACCAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.30, C:0.22, G:0.00, T:0.48
Consensus pattern (16 bp):
TCTATTCTATTACAAC
Found at i:10321341 original size:45 final size:45
Alignment explanation
Indices: 10321292--10321384 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 45
10321282 GTCTAAACTC
* * *
10321292 AAAAAA-GTAAATCTTATTTTCTTCAAAATAAAAAATAAAACAATT
1 AAAAAATGT-AATATTATTTGCCTCAAAATAAAAAATAAAACAATT
*
10321337 AAAAAATGTAATATTATTTGCCTCAAAATAAAAAATAAAATAATT
1 AAAAAATGTAATATTATTTGCCTCAAAATAAAAAATAAAACAATT
10321382 AAA
1 AAA
10321385 TTAAATTCGG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
45 41 0.95
46 2 0.05
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.30
Consensus pattern (45 bp):
AAAAAATGTAATATTATTTGCCTCAAAATAAAAAATAAAACAATT
Found at i:10321425 original size:5 final size:5
Alignment explanation
Indices: 10321392--10321421 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
10321382 AAATTAAATT
*
10321392 CGGGG CGGGG CGGGG CGGGG CGGGG TGGGG
1 CGGGG CGGGG CGGGG CGGGG CGGGG CGGGG
10321422 TGGGTCAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.80, T:0.03
Consensus pattern (5 bp):
CGGGG
Found at i:10324749 original size:16 final size:18
Alignment explanation
Indices: 10324720--10324752 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
10324710 TAAAAAAAGC
10324720 TTAACATTTCAAAAAATT
1 TTAACATTTCAAAAAATT
10324738 TTAA-ATTT-AAAAAAT
1 TTAACATTTCAAAAAAT
10324753 AAGTATTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (18 bp):
TTAACATTTCAAAAAATT
Found at i:10334649 original size:19 final size:20
Alignment explanation
Indices: 10334605--10334650 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
10334595 AGATTACCAG
*
10334605 CTCAAAATAAATTTTGGATT
1 CTCAAAATAAATTTTGGAAT
10334625 CTCAAAAT-AATTTTCGGAAT
1 CTCAAAATAAATTTT-GGAAT
10334645 C-CAAAA
1 CTCAAAA
10334651 ATGAGAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.33
Consensus pattern (20 bp):
CTCAAAATAAATTTTGGAAT
Found at i:10335328 original size:13 final size:13
Alignment explanation
Indices: 10335310--10335335 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10335300 CTTTCTGTCT
10335310 GTCCCTCTTCCTC
1 GTCCCTCTTCCTC
10335323 GTCCCTCTTCCTC
1 GTCCCTCTTCCTC
10335336 TCTTTCTCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.54, G:0.08, T:0.38
Consensus pattern (13 bp):
GTCCCTCTTCCTC
Found at i:10345921 original size:16 final size:16
Alignment explanation
Indices: 10345900--10345970 Score: 115
Period size: 16 Copynumber: 4.4 Consensus size: 16
10345890 GTTTAGTTCA
10345900 CTGTAATGGAATAGGG
1 CTGTAATGGAATAGGG
*
10345916 CTGTAATTGAATAGGG
1 CTGTAATGGAATAGGG
*
10345932 CTGTAATTGAATAGGG
1 CTGTAATGGAATAGGG
*
10345948 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGGG
10345964 CTGTAAT
1 CTGTAAT
10345971 CAGTAATTCA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.32, C:0.07, G:0.31, T:0.30
Consensus pattern (16 bp):
CTGTAATGGAATAGGG
Found at i:10346559 original size:13 final size:12
Alignment explanation
Indices: 10346541--10346595 Score: 65
Period size: 13 Copynumber: 4.2 Consensus size: 12
10346531 CACACACCGG
10346541 AAGAGAGAAAGAA
1 AAGA-AGAAAGAA
10346554 AAGAGAGAAAGGAA
1 AAGA-AGAAA-GAA
10346568 AAGAAGAGAAGAA
1 AAGAAGA-AAGAA
10346581 GAAGAAGAAAGAA
1 -AAGAAGAAAGAA
10346594 AA
1 AA
10346596 AAATAAAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
12 2 0.05
13 21 0.54
14 16 0.41
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (12 bp):
AAGAAGAAAGAA
Found at i:10346588 original size:17 final size:16
Alignment explanation
Indices: 10346540--10346593 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 16
10346530 CCACACACCG
10346540 GAAGAG-AGAAAGAAAA
1 GAAGAGAAG-AAGAAAA
*
10346556 G-AGAGAA-AGGAAAA
1 GAAGAGAAGAAGAAAA
10346570 GAAGAGAAGAAGAAGAA
1 GAAGAGAAGAAGAA-AA
10346587 GAA-AGAA
1 GAAGAGAA
10346594 AAAAATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
14 7 0.22
15 10 0.31
16 10 0.31
17 5 0.16
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (16 bp):
GAAGAGAAGAAGAAAA
Found at i:10346807 original size:33 final size:32
Alignment explanation
Indices: 10346770--10346866 Score: 89
Period size: 33 Copynumber: 3.1 Consensus size: 32
10346760 GTTTTTTATA
10346770 ATTATTTTAAAATTAATTTGTTAGTAATTTAAG
1 ATTATTTTAAAATTAATTT-TTAGTAATTTAAG
* * *
10346803 ATTATGTT-AAATT--TTTTT-GT-GTTTGTA-
1 ATTATTTTAAAATTAATTTTTAGTAATTT-AAG
*
10346830 ATTATTTTAAAATTAATTTATTAGTAATTTAGG
1 ATTATTTTAAAATTAATTT-TTAGTAATTTAAG
10346863 ATTA
1 ATTA
10346867 AGTTATAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
27 10 0.20
28 8 0.16
29 2 0.04
30 6 0.12
31 2 0.04
32 7 0.14
33 14 0.29
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (32 bp):
ATTATTTTAAAATTAATTTTTAGTAATTTAAG
Found at i:10346843 original size:60 final size:61
Alignment explanation
Indices: 10346749--10346871 Score: 194
Period size: 60 Copynumber: 2.0 Consensus size: 61
10346739 TGTATGAATG
* * *
10346749 TAAATTTTTTTGTTTTTTATAATTATTTTAAAATTAATTTGTTAGTAATTTAAGATTATGT
1 TAAATTTTTTTGTTGTTTATAATTATTTTAAAATTAATTTATTAGTAATTTAAGATTAAGT
* *
10346810 TAAATTTTTTTG-TGTTTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGT
1 TAAATTTTTTTGTTGTTTATAATTATTTTAAAATTAATTTATTAGTAATTTAAGATTAAGT
10346870 TA
1 TA
10346872 TAAATTGTTG
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
60 45 0.79
61 12 0.21
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (61 bp):
TAAATTTTTTTGTTGTTTATAATTATTTTAAAATTAATTTATTAGTAATTTAAGATTAAGT
Found at i:10346883 original size:60 final size:60
Alignment explanation
Indices: 10346768--10346886 Score: 177
Period size: 60 Copynumber: 2.0 Consensus size: 60
10346758 TTGTTTTTTA
* * * *
10346768 TAATTATTTTAAAATTAATTTGTTAGTAATTTAAGATTATGTTAAATTTTTTTGTGTTTG
1 TAATTATTTTAAAATTAATTTATTAGTAATTTAAGATTAAGTTAAATATTGTTGTGTTTG
*
10346828 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAA-ATTGTTGTGTTT
1 TAATTATTTTAAAATTAATTTATTAGTAATTTAAGATTAAGTTA-AATATTGTTGTGTTT
10346887 AGTTTAGTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
60 51 0.96
61 2 0.04
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.55
Consensus pattern (60 bp):
TAATTATTTTAAAATTAATTTATTAGTAATTTAAGATTAAGTTAAATATTGTTGTGTTTG
Found at i:10348057 original size:15 final size:15
Alignment explanation
Indices: 10348037--10348096 Score: 61
Period size: 15 Copynumber: 4.0 Consensus size: 15
10348027 TTCTATTTCT
10348037 ATTTTTATTTTTTTA
1 ATTTTTATTTTTTTA
*
10348052 ATTTTT-TCTATTTCT-
1 ATTTTTAT-T-TTTTTA
10348067 ATTTTTATTTTTTTA
1 ATTTTTATTTTTTTA
* *
10348082 ATTTGTATGTTTTTA
1 ATTTTTATTTTTTTA
10348097 TGTTTACATA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 5 0.14
15 27 0.73
16 5 0.14
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.75
Consensus pattern (15 bp):
ATTTTTATTTTTTTA
Found at i:10348062 original size:30 final size:30
Alignment explanation
Indices: 10348026--10348085 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
10348016 ATCAGGTATG
10348026 TTTCTATTTCTATTTTTATTTTTTTAATTT
1 TTTCTATTTCTATTTTTATTTTTTTAATTT
10348056 TTTCTATTTCTATTTTTATTTTTTTAATTT
1 TTTCTATTTCTATTTTTATTTTTTTAATTT
10348086 GTATGTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.77
Consensus pattern (30 bp):
TTTCTATTTCTATTTTTATTTTTTTAATTT
Found at i:10348085 original size:21 final size:22
Alignment explanation
Indices: 10348032--10348080 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
10348022 TATGTTTCTA
*
10348032 TTTCTATTTTTATTTTTTTAATTT
1 TTTCTATTTCTA--TTTTTAATTT
*
10348056 TTTCTATTTCTATTTTTATTTT
1 TTTCTATTTCTATTTTTAATTT
10348078 TTT
1 TTT
10348081 AATTTGTATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 12 0.52
24 11 0.48
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTCTATTTCTATTTTTAATTT
Found at i:10350370 original size:75 final size:73
Alignment explanation
Indices: 10350211--10350374 Score: 188
Period size: 75 Copynumber: 2.2 Consensus size: 73
10350201 TTTTGTAATG
* *
10350211 TAAATAACTTCATATTTATGTAATGAATTTTTTGGCATTTTATTTATCAATTTATTTATTTATTT
1 TAAATAACTTTATATTTATATAATGAATTTTTTGGCATTTTATTTATCAATTTATTTATTTATTT
10350276 GCAATTTAAA
66 --AATTTAAA
** * * * *
10350286 TAGTTAACTTTATATTTATATAATGACTTTTTTGTCATTTTTTTTATCAATTTTATGGTTTTTTA
1 TAAATAACTTTATATTTATATAATGAATTTTTTGGCATTTTATTTATCAA-TTTAT--TTATTTA
10350351 -TT-ATTTAAA
63 TTTAATTTAAA
10350360 TAAATAAACTTTATA
1 TAAAT-AACTTTATA
10350375 CTAACTATGT
Statistics
Matches: 75, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
74 10 0.13
75 52 0.69
76 5 0.07
77 2 0.03
78 6 0.08
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (73 bp):
TAAATAACTTTATATTTATATAATGAATTTTTTGGCATTTTATTTATCAATTTATTTATTTATTT
AATTTAAA
Found at i:10353501 original size:27 final size:27
Alignment explanation
Indices: 10353462--10353539 Score: 111
Period size: 27 Copynumber: 2.9 Consensus size: 27
10353452 TGTGGGCCCC
*
10353462 ACCATTTGCGCCTCTGGGATAGGCACA
1 ACCATTTGCGCCTCTGAGATAGGCACA
* *
10353489 ACCATTTGTGCCTCTGAGATAGGCATA
1 ACCATTTGCGCCTCTGAGATAGGCACA
* *
10353516 ACCATTTGCGCCTCAGAGAAAGGC
1 ACCATTTGCGCCTCTGAGATAGGC
10353540 TCAATTAGTC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.23
Consensus pattern (27 bp):
ACCATTTGCGCCTCTGAGATAGGCACA
Found at i:10354013 original size:58 final size:57
Alignment explanation
Indices: 10353878--10354015 Score: 163
Period size: 58 Copynumber: 2.4 Consensus size: 57
10353868 ATTGTTATTG
*
10353878 TTATTAAATTTTAATA-AGATTATTATTAAAAATAATTTAATAAAAATAATAAATAAT
1 TTATTAAATTTTAATATA-ATTACTATTAAAAATAATTTAATAAAAATAATAAATAAT
** * * * *
10353935 TTAACCATATTTTAACATAATTACTATTAAATATAATTTAAT-AAAATAATATATAAT
1 TT-ATTAAATTTTAATATAATTACTATTAAAAATAATTTAATAAAAATAATAAATAAT
10353992 TTATTAAAATTCTTAATATAATTA
1 TTATT-AAATT-TTAATATAATTA
10354016 TTATATGAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
56 1 0.02
57 22 0.33
58 42 0.64
59 1 0.02
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (57 bp):
TTATTAAATTTTAATATAATTACTATTAAAAATAATTTAATAAAAATAATAAATAAT
Found at i:10362504 original size:135 final size:135
Alignment explanation
Indices: 10362262--10362527 Score: 397
Period size: 135 Copynumber: 2.0 Consensus size: 135
10362252 CCAATTTACT
* * * * *
10362262 TGCAGGGGAAGAGTTTCAACTTTGCTTGGCAGTGATTTCCGAGATACAATGGACCGATTAATGAC
1 TGCAGGGGAAGAGTTTCAACTTTACTTGACAGTGATTTCCGAGAGAAAATGAACCGATTAATGAC
* *
10362327 TTCTCGTGTACAGATCCAAGCGGATGGGGCAGAAAGTCAACAAGAAGTGGATGATAAGGAAGGAA
66 TTCTCGTGTACAAATCCAAGCGGATGGGGCAGAAAGTCAACAAGAAGTGGAGGATAAGGAAGGAA
10362392 TTATA
131 TTATA
* *
10362397 TGCAGGGGAAGAGTTTCAACTTTATTTGACAGTGATTTCCTAGAGAAAATGAACCGATTAATGAC
1 TGCAGGGGAAGAGTTTCAACTTTACTTGACAGTGATTTCCGAGAGAAAATGAACCGATTAATGAC
* * ** * *
10362462 TTCTCGTGTACAAATGCAAGCTGATGTTGCTGAAAGTCAACAAGAAGTTGAGGATAAGGAAGGAA
66 TTCTCGTGTACAAATCCAAGCGGATGGGGCAGAAAGTCAACAAGAAGTGGAGGATAAGGAAGGAA
10362527 T
131 T
10362528 GGTCCAACGA
Statistics
Matches: 116, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
135 116 1.00
ACGTcount: A:0.34, C:0.14, G:0.27, T:0.25
Consensus pattern (135 bp):
TGCAGGGGAAGAGTTTCAACTTTACTTGACAGTGATTTCCGAGAGAAAATGAACCGATTAATGAC
TTCTCGTGTACAAATCCAAGCGGATGGGGCAGAAAGTCAACAAGAAGTGGAGGATAAGGAAGGAA
TTATA
Found at i:10362591 original size:3 final size:3
Alignment explanation
Indices: 10362547--10362573 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
10362537 AGTGTCTTAC
10362547 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
10362574 TACGACGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:10365632 original size:9 final size:9
Alignment explanation
Indices: 10365596--10365642 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
10365586 TTTATTGTAA
10365596 TTTTA-ATT
1 TTTTATATT
* *
10365604 TTTAATAAT
1 TTTTATATT
*
10365613 TTATATATT
1 TTTTATATT
*
10365622 TTTTGTATT
1 TTTTATATT
10365631 TTTTATATT
1 TTTTATATT
10365640 TTT
1 TTT
10365643 CAAGCAGAAG
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
8 4 0.13
9 26 0.87
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (9 bp):
TTTTATATT
Found at i:10366133 original size:28 final size:28
Alignment explanation
Indices: 10366101--10366163 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
10366091 TCCTATATTA
10366101 ATGGGGTATAGGAAAAATCTCATAACTT
1 ATGGGGTATAGGAAAAATCTCATAACTT
* * * *
10366129 ATGGGGTATAGGAAGAGTTTTATAACTT
1 ATGGGGTATAGGAAAAATCTCATAACTT
10366157 ATGGGGT
1 ATGGGGT
10366164 TGATAATGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.33, C:0.06, G:0.29, T:0.32
Consensus pattern (28 bp):
ATGGGGTATAGGAAAAATCTCATAACTT
Found at i:10371520 original size:28 final size:28
Alignment explanation
Indices: 10371489--10371551 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
10371479 TCCCATATTA
10371489 ATGGGGTATAGGAAAAG-TCTCATAACTT
1 ATGGGGTATAGGAAAAGAT-TCATAACTT
* *
10371517 ATGGGGTATAGGAAGAGATTTATAACTT
1 ATGGGGTATAGGAAAAGATTCATAACTT
10371545 ATGGGGT
1 ATGGGGT
10371552 TGATAATGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 31 0.97
29 1 0.03
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.30
Consensus pattern (28 bp):
ATGGGGTATAGGAAAAGATTCATAACTT
Found at i:10379714 original size:31 final size:31
Alignment explanation
Indices: 10379652--10379717 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
10379642 TAACATCCTT
* *
10379652 ATAACTTAAATAAAAACTTCTGAGTAGTTTA
1 ATAACTTAAATAAAAACTTCTGAATAATTTA
*** *
10379683 ATAACTTAAATAAATTTTTTTGAATAATTTA
1 ATAACTTAAATAAAAACTTCTGAATAATTTA
10379714 ATAA
1 ATAA
10379718 TTATTTTGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (31 bp):
ATAACTTAAATAAAAACTTCTGAATAATTTA
Found at i:10388707 original size:53 final size:53
Alignment explanation
Indices: 10388626--10388776 Score: 196
Period size: 53 Copynumber: 2.8 Consensus size: 53
10388616 CTTACACGGT
* *
10388626 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
10388681 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
* ** * *
10388734 TTACATTGCACCGATGTCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
10388777 GCGCACTTAT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
52 1 0.01
53 79 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:10390953 original size:18 final size:18
Alignment explanation
Indices: 10390930--10390965 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
10390920 GGTTCCAAAG
* *
10390930 ATAAAAATTATCTTAAAA
1 ATAAAAATAATATTAAAA
10390948 ATAAAAATAATATTAAAA
1 ATAAAAATAATATTAAAA
10390966 TGGTCATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAAAAATAATATTAAAA
Found at i:10391410 original size:25 final size:25
Alignment explanation
Indices: 10391381--10391435 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
10391371 TATGAAAGGT
* *
10391381 ATAACATTCTTTTATGGTGGGTGCA
1 ATAACATTCTTTTATAGTGGATGCA
*
10391406 ATAACTTTCTTTTATAGTGGATGCA
1 ATAACATTCTTTTATAGTGGATGCA
10391431 ATAAC
1 ATAAC
10391436 CTTTAGATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (25 bp):
ATAACATTCTTTTATAGTGGATGCA
Found at i:10392483 original size:16 final size:16
Alignment explanation
Indices: 10392461--10392497 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
10392451 ATCAAATATA
10392461 TTTAAAAA-ATTAAAT
1 TTTAAAAATATTAAAT
10392476 TGTTAAAAATATTAAAT
1 T-TTAAAAATATTAAAT
10392493 TTTAA
1 TTTAA
10392498 TTAATTGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 1 0.05
16 11 0.55
17 8 0.40
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
TTTAAAAATATTAAAT
Found at i:10407787 original size:40 final size:40
Alignment explanation
Indices: 10407742--10407823 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
10407732 TAAGAAAATA
10407742 TCTTATCAAATAATAAAGAACCTTAGACGCATTAATGTAC
1 TCTTATCAAATAATAAAGAACCTTAGACGCATTAATGTAC
10407782 TCTTATCAAATAATAAAGAACCTTAGACGCATTAATGTAC
1 TCTTATCAAATAATAAAGAACCTTAGACGCATTAATGTAC
10407822 TC
1 TC
10407824 CAAATACTAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.30
Consensus pattern (40 bp):
TCTTATCAAATAATAAAGAACCTTAGACGCATTAATGTAC
Found at i:10414175 original size:17 final size:17
Alignment explanation
Indices: 10414153--10414187 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
10414143 GATTGATAAA
10414153 ATATGTGAAAGTTTCGT
1 ATATGTGAAAGTTTCGT
*
10414170 ATATGTGACAGTTTCGT
1 ATATGTGAAAGTTTCGT
10414187 A
1 A
10414188 AAGAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.09, G:0.23, T:0.40
Consensus pattern (17 bp):
ATATGTGAAAGTTTCGT
Found at i:10415168 original size:14 final size:15
Alignment explanation
Indices: 10415147--10415192 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
10415137 TTACAATGGT
10415147 TGAATTGAATGTATA
1 TGAATTGAATGTATA
*
10415162 T-AATTGAAT-TATT
1 TGAATTGAATGTATA
10415175 TGAGATATGAATGTATA
1 TGA-AT-TGAATGTATA
10415192 T
1 T
10415193 TTACAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 4 0.16
14 9 0.36
15 3 0.12
16 5 0.20
17 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.43
Consensus pattern (15 bp):
TGAATTGAATGTATA
Found at i:10416259 original size:30 final size:31
Alignment explanation
Indices: 10416225--10416293 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
10416215 TGGCCCAAGA
*
10416225 GTAAATATTCAAAATTT-AAGGGATTAA-AGT
1 GTAAATATTCAAAATTTGAA-GGACTAATAGT
*
10416255 GTAAATA-TGAAAATTTGAAGGACTAATAGT
1 GTAAATATTCAAAATTTGAAGGACTAATAGT
*
10416285 GCAAATATT
1 GTAAATATT
10416294 TTAAGGTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
29 14 0.42
30 18 0.55
31 1 0.03
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.32
Consensus pattern (31 bp):
GTAAATATTCAAAATTTGAAGGACTAATAGT
Found at i:10420259 original size:33 final size:33
Alignment explanation
Indices: 10420134--10420259 Score: 80
Period size: 33 Copynumber: 3.8 Consensus size: 33
10420124 ATCGTTTTCT
* *
10420134 TGATGCCATAGTCCAACTATGGTCTTA-CA-CGTA
1 TGATGCCATAGCCCAGCTATGGTCTTATCATC--A
* ** * *
10420167 T-ATTGCCATGGCCGTGCCATGGTCTTAT-ACTCG
1 TGA-TGCCATAGCCCAGCTATGGTCTTATCA-TCA
* * * * *
10420200 TAATGCCATAACCTAGTTATGATCTTATCATCA
1 TGATGCCATAGCCCAGCTATGGTCTTATCATCA
10420233 TGATGCCATAGCCCAGCTATGGTCTTA
1 TGATGCCATAGCCCAGCTATGGTCTTA
10420260 CACATGTACA
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
32 1 0.01
33 63 0.94
34 2 0.03
35 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.33
Consensus pattern (33 bp):
TGATGCCATAGCCCAGCTATGGTCTTATCATCA
Found at i:10423593 original size:17 final size:17
Alignment explanation
Indices: 10423571--10423607 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
10423561 AAGACCAATA
10423571 GTGCAAATATTTTAAAG
1 GTGCAAATATTTTAAAG
*
10423588 GTGCAAATATTTTAAGG
1 GTGCAAATATTTTAAAG
10423605 GTG
1 GTG
10423608 GAATGATCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.35
Consensus pattern (17 bp):
GTGCAAATATTTTAAAG
Found at i:10423852 original size:11 final size:11
Alignment explanation
Indices: 10423838--10423881 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
10423828 AGATAAATAT
10423838 TATTTTATTAA
1 TATTTTATTAA
*
10423849 TATTTTGATGAGA
1 TATTTT-ATTA-A
*
10423862 TATTTTATTAT
1 TATTTTATTAA
10423873 TATTTTATT
1 TATTTTATT
10423882 TAGTATATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
11 15 0.54
12 6 0.21
13 7 0.25
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:10425341 original size:25 final size:27
Alignment explanation
Indices: 10425304--10425356 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
10425294 TCAAACATGC
10425304 ATTTAGGTCAATTTA-ATCCTAGGGGT
1 ATTTAGGTCAATTTATATCCTAGGGGT
* *
10425330 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTATATCCTAGGGGT
10425356 A
1 A
10425357 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.40
Consensus pattern (27 bp):
ATTTAGGTCAATTTATATCCTAGGGGT
Found at i:10426886 original size:32 final size:32
Alignment explanation
Indices: 10426849--10426913 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
10426839 AATGCTTACC
10426849 ATGCCCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
10426881 ATGCCCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
10426913 A
1 A
10426914 AATGCATACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (32 bp):
ATGCCCATCATCCATTAACTATTAAAATGCTA
Found at i:10436844 original size:29 final size:30
Alignment explanation
Indices: 10436802--10436860 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
10436792 TATGATTTAA
*
10436802 TGTGTAATTCTATACATG-AATTTTGATTT
1 TGTGCAATTCTATACATGAAATTTTGATTT
* *
10436831 TGTGCAATTTTATACTTGAAATTTTGATTT
1 TGTGCAATTCTATACATGAAATTTTGATTT
10436861 GATCCAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.27, C:0.07, G:0.14, T:0.53
Consensus pattern (30 bp):
TGTGCAATTCTATACATGAAATTTTGATTT
Found at i:10436869 original size:30 final size:29
Alignment explanation
Indices: 10436807--10436875 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
10436797 TTTAATGTGT
* *
10436807 AATTCTATACATGAATTTTGATTTTGTGC
1 AATTTTATACATGAATTTTGATTTTGTCC
*
10436836 AATTTTATACTTGAAATTTTGA-TTTGATCC
1 AATTTTATACATG-AATTTTGATTTTG-TCC
10436866 AATTCTTATA
1 AATT-TTATA
10436876 AATTATTAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 15 0.44
30 14 0.41
31 5 0.15
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.49
Consensus pattern (29 bp):
AATTTTATACATGAATTTTGATTTTGTCC
Found at i:10440733 original size:21 final size:21
Alignment explanation
Indices: 10440677--10440733 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
10440667 TCATGGGCTG
* *
10440677 TTCACATGGGCATGTGTCCCA
1 TTCACATGGGCGTGTGTACCA
* * *
10440698 TTTACACGGGTGTGTGTGACC-
1 TTCACATGGGCGTGTGT-ACCA
10440719 TTCACATGGGCGTGT
1 TTCACATGGGCGTGT
10440734 AGACCTCTAC
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
21 25 0.93
22 2 0.07
ACGTcount: A:0.16, C:0.23, G:0.30, T:0.32
Consensus pattern (21 bp):
TTCACATGGGCGTGTGTACCA
Found at i:10447804 original size:22 final size:23
Alignment explanation
Indices: 10447779--10447831 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
10447769 GTGGAATTAA
10447779 AAAAAAAATTATCTT-AATTTAT
1 AAAAAAAATTATCTTAAATTTAT
* * * *
10447801 AAAAATACTTGTCTTAAATTTTT
1 AAAAAAAATTATCTTAAATTTAT
10447824 AAAAAAAA
1 AAAAAAAA
10447832 AGTAATTTAA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.38
Consensus pattern (23 bp):
AAAAAAAATTATCTTAAATTTAT
Found at i:10457093 original size:8 final size:8
Alignment explanation
Indices: 10457051--10457075 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
10457041 ATATAGACTA
10457051 AATAAAAT
1 AATAAAAT
10457059 AATAAAAT
1 AATAAAAT
10457067 AATAAAAT
1 AATAAAAT
10457075 A
1 A
10457076 TCTTATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:10457099 original size:29 final size:31
Alignment explanation
Indices: 10457048--10457116 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 31
10457038 TATATATAGA
*
10457048 CTAAATAAAATAATAAAATAATAA-AA-TAT
1 CTAATTAAAATAATAAAATAATAATAATTAT
* *
10457077 CTTATTAAAAT-ATTAAATAAATAATAATTAT
1 CTAATTAAAATAATAAAAT-AATAATAATTAT
10457108 CTAATTAAA
1 CTAATTAAA
10457117 TAACTATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 6 0.18
29 14 0.42
30 2 0.06
31 11 0.33
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (31 bp):
CTAATTAAAATAATAAAATAATAATAATTAT
Found at i:10457394 original size:30 final size:30
Alignment explanation
Indices: 10457329--10457386 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
10457319 TACCCTTAAA
* *
10457329 ATATTTGCACTATTAGTCCTTAAACTTTTC
1 ATATTTGCACTATTAATCCTCAAACTTTTC
10457359 ATATTTGCACT-TTAATCCCTCAAA-TTTT
1 ATATTTGCACTATTAAT-CCTCAAACTTTT
10457387 GAGTATTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.28, C:0.21, G:0.05, T:0.47
Consensus pattern (30 bp):
ATATTTGCACTATTAATCCTCAAACTTTTC
Found at i:10458307 original size:29 final size:30
Alignment explanation
Indices: 10458260--10458327 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
10458250 TGGCCCAAAA
* *
10458260 GTAAATACTCAAAATTTGAAGGATTAA-AGT
1 GTAAATA-TCAAAAGTTGAAGGACTAATAGT
*
10458290 GTAAATATGAAAAGTTGAAGGACTAATAGT
1 GTAAATATCAAAAGTTGAAGGACTAATAGT
*
10458320 GCAAATAT
1 GTAAATAT
10458328 TTTAAGGGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (30 bp):
GTAAATATCAAAAGTTGAAGGACTAATAGT
Found at i:10460808 original size:46 final size:46
Alignment explanation
Indices: 10460751--10460978 Score: 341
Period size: 46 Copynumber: 5.0 Consensus size: 46
10460741 AGTGTGCTCT
* **
10460751 CTGAAATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCGGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
10460797 CTGATATGAAATGTGTAAGACTATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
10460843 CTGATATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
10460889 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
10460935 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
10460979 TCATGTCAAA
Statistics
Matches: 168, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 1 0.01
46 167 0.99
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:10464247 original size:37 final size:37
Alignment explanation
Indices: 10464206--10464276 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
10464196 TCCGATGCCA
10464206 TAGTCCAACTATGGTCTTATACATACATTGCCAAGGC
1 TAGTCCAACTATGGTCTTATACATACATTGCCAAGGC
10464243 TAGTCCAACTATGGTCTTATACATACATTGCCAA
1 TAGTCCAACTATGGTCTTATACATACATTGCCAA
10464277 CGCCCTGCCG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (37 bp):
TAGTCCAACTATGGTCTTATACATACATTGCCAAGGC
Found at i:10464395 original size:33 final size:33
Alignment explanation
Indices: 10464318--10464395 Score: 113
Period size: 33 Copynumber: 2.4 Consensus size: 33
10464308 ATAACTTGGT
*
10464318 TATGGTCTTTTTAGTCGATTGCCATAGTCCCGC
1 TATGGTCTTATTAGTCGATTGCCATAGTCCCGC
* *
10464351 TATGGTTTTATTATTCGATTGCCATAG-CCCAGC
1 TATGGTCTTATTAGTCGATTGCCATAGTCCC-GC
10464384 TATGGTCTTATT
1 TATGGTCTTATT
10464396 TGACAACTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 3 0.08
33 37 0.93
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.42
Consensus pattern (33 bp):
TATGGTCTTATTAGTCGATTGCCATAGTCCCGC
Found at i:10464893 original size:43 final size:43
Alignment explanation
Indices: 10464870--10464984 Score: 137
Period size: 43 Copynumber: 2.7 Consensus size: 43
10464860 ATCTCATATC
* *
10464870 GATGCCAATGTCCTAGACATGGTCTTAAACGAAATCATATAAT
1 GATGCCAATGTCCCAGACATGGTCTTACACGAAATCATATAAT
*
10464913 GATGCCAATGTCCCAGACATGGTCTTACAC-ATAATAATAGTACA-
1 GATGCCAATGTCCCAGACATGGTCTTACACGA-AATCATA-TA-AT
**
10464957 -ATGCCAATGTCCCAGACATTTTCTTACA
1 GATGCCAATGTCCCAGACATGGTCTTACA
10464985 TGTAATCTCA
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
42 1 0.02
43 60 0.94
44 2 0.03
45 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.28
Consensus pattern (43 bp):
GATGCCAATGTCCCAGACATGGTCTTACACGAAATCATATAAT
Found at i:10468113 original size:52 final size:48
Alignment explanation
Indices: 10468094--10468394 Score: 366
Period size: 46 Copynumber: 6.3 Consensus size: 48
10468084 TGACAAGTGG
* *
10468094 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
* **
10468140 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
* *
10468188 GTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 ----AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
10468238 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
10468290 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
10468336 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
10468382 AAAGTGATAAGTG
1 AAAGTGATAAGTG
10468395 GATACACTTA
Statistics
Matches: 226, Mismatches: 17, Indels: 24
0.85 0.06 0.09
Matches are distributed among these distances:
46 141 0.62
52 85 0.38
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:10468148 original size:98 final size:98
Alignment explanation
Indices: 10468028--10468383 Score: 640
Period size: 98 Copynumber: 3.6 Consensus size: 98
10468018 TTTGAGTACT
*
10468028 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
10468093 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
*
10468126 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
10468191 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
10468224 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
* *
10468289 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
10468322 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAA
10468384 AGTGATAAGT
Statistics
Matches: 249, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 249 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:10468404 original size:37 final size:37
Alignment explanation
Indices: 10468358--10468503 Score: 233
Period size: 37 Copynumber: 4.0 Consensus size: 37
10468348 GATAGCTTTA
*
10468358 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
10468395 GATACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
10468432 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
10468469 GCTACACTTATCTGATC-AGTGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
10468504 ATCATACGTA
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 87 0.85
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:10469832 original size:58 final size:58
Alignment explanation
Indices: 10469755--10469922 Score: 237
Period size: 58 Copynumber: 3.0 Consensus size: 58
10469745 CATGTGAACA
10469755 TGTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
1 TGTGA-TATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
10469814 TGTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATA--
1 TGTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
* * *
10469870 TGTG--A--T--TT-CGTGTAAGACCATAGTTGGGCTATGGCATCGGTATGTGATTTG
1 TGTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
10469921 TG
1 TG
10469923 ATTACGTGTA
Statistics
Matches: 104, Mismatches: 3, Indels: 12
0.87 0.03 0.10
Matches are distributed among these distances:
49 38 0.37
50 2 0.02
51 2 0.02
52 1 0.01
54 1 0.01
56 4 0.04
58 51 0.49
59 5 0.05
ACGTcount: A:0.23, C:0.13, G:0.31, T:0.33
Consensus pattern (58 bp):
TGTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
Found at i:10469864 original size:28 final size:28
Alignment explanation
Indices: 10469774--10469864 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 28
10469764 GTGATTCCGT
10469774 GTAAGACCATAGCTGGGCTATGGCATCG
1 GTAAGACCATAGCTGGGCTATGGCATCG
** * *
10469802 GTAAG-TGATATG-TGTGATATGTG-ATTCCG
1 GTAAGACCATA-GCTGGGCTATG-GCA-T-CG
10469831 TGTAAGACCATAGCTGGGCTATGGCATCG
1 -GTAAGACCATAGCTGGGCTATGGCATCG
10469860 GTAAG
1 GTAAG
10469865 TGATATGTGA
Statistics
Matches: 47, Mismatches: 8, Indels: 16
0.66 0.11 0.23
Matches are distributed among these distances:
27 11 0.23
28 13 0.28
29 4 0.09
30 8 0.17
31 11 0.23
ACGTcount: A:0.25, C:0.15, G:0.32, T:0.27
Consensus pattern (28 bp):
GTAAGACCATAGCTGGGCTATGGCATCG
Found at i:10469887 original size:49 final size:49
Alignment explanation
Indices: 10469815--10469957 Score: 232
Period size: 49 Copynumber: 2.9 Consensus size: 49
10469805 AGTGATATGT
* *
10469815 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
* *
10469864 GTGATATGTGATTTCGTGTAAGACCATAGTTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
* *
10469913 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCG
10469958 AGAAAACAAA
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 88 1.00
ACGTcount: A:0.24, C:0.14, G:0.30, T:0.32
Consensus pattern (49 bp):
GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
Found at i:10473137 original size:12 final size:13
Alignment explanation
Indices: 10473118--10473150 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
10473108 GGGTTCGGCT
10473118 ATGGAGAAGGAAG
1 ATGGAGAAGGAAG
*
10473131 A-GGAGAAGGTAG
1 ATGGAGAAGGAAG
10473143 ATGGAGAA
1 ATGGAGAA
10473151 AAAGAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.45, C:0.00, G:0.45, T:0.09
Consensus pattern (13 bp):
ATGGAGAAGGAAG
Found at i:10473764 original size:9 final size:9
Alignment explanation
Indices: 10473750--10473775 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
10473740 AGAGTTAAAG
10473750 ATTCTAGAC
1 ATTCTAGAC
10473759 ATTCTAGAC
1 ATTCTAGAC
10473768 ATTCTAGA
1 ATTCTAGA
10473776 TATACGTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (9 bp):
ATTCTAGAC
Found at i:10476643 original size:13 final size:13
Alignment explanation
Indices: 10476625--10476649 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10476615 TAGTAACATT
10476625 TTAAATATATGTG
1 TTAAATATATGTG
10476638 TTAAATATATGT
1 TTAAATATATGT
10476650 TATGTTCATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAAATATATGTG
Found at i:10486339 original size:15 final size:15
Alignment explanation
Indices: 10486289--10486338 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
10486279 AAAAAGACAA
10486289 AAGAAAATCAAACAA-
1 AAGAAAATCAAA-AAG
*
10486304 AAGAAAATAAAAAAG
1 AAGAAAATCAAAAAG
*
10486319 AAGAATATCAAAAAG
1 AAGAAAATCAAAAAG
10486334 AAGAA
1 AAGAA
10486339 TTTGAGAGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
14 2 0.06
15 29 0.94
ACGTcount: A:0.74, C:0.06, G:0.12, T:0.08
Consensus pattern (15 bp):
AAGAAAATCAAAAAG
Found at i:10488396 original size:3 final size:3
Alignment explanation
Indices: 10488381--10488443 Score: 56
Period size: 3 Copynumber: 20.7 Consensus size: 3
10488371 TGCAGCAGCA
* * *
10488381 AAG AGAG AA- AAG AAG AAG AAG AAA AAG AAA AAG AAG AAG AAG GAG
1 AAG A-AG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* *
10488426 AAG GAG GAG AAAG AAG AA
1 AAG AAG AAG -AAG AAG AA
10488444 AAAAATGTTA
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
2 2 0.04
3 42 0.86
4 5 0.10
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:10491823 original size:28 final size:27
Alignment explanation
Indices: 10491762--10491913 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
10491752 ATATTAAGTC
* *
10491762 CGCACACTCAGTGCTATATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
10491789 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
10491817 CGCACACTTAGTGCTACCTAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
10491844 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
10491872 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
10491899 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
10491914 GCACAATTTA
Statistics
Matches: 116, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
27 64 0.55
28 52 0.45
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:10491830 original size:55 final size:55
Alignment explanation
Indices: 10491762--10491913 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
10491752 ATATTAAGTC
* *
10491762 CGCACACTCAGTGCTATATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
* *
10491817 CGCACACTTAGTGCTACCTAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
10491872 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
10491914 GCACAATTTA
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 91 1.00
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:10494435 original size:6 final size:6
Alignment explanation
Indices: 10494424--10494475 Score: 68
Period size: 6 Copynumber: 8.7 Consensus size: 6
10494414 ACCAACTCCG
* * * *
10494424 GAGCCA GAGCCA GAGCCA GAGCCA GAGCCG GAGGCA GTGCCA GACCCA
1 GAGCCA GAGCCA GAGCCA GAGCCA GAGCCA GAGCCA GAGCCA GAGCCA
10494472 GAGC
1 GAGC
10494476 GGCGGCCAGA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.29, C:0.33, G:0.37, T:0.02
Consensus pattern (6 bp):
GAGCCA
Found at i:10494493 original size:18 final size:20
Alignment explanation
Indices: 10494426--10494493 Score: 58
Period size: 18 Copynumber: 3.7 Consensus size: 20
10494416 CAACTCCGGA
* *
10494426 GCCAGAGCCAGAGC--CAGA
1 GCCAGAGCCGGAGCGGCAGT
10494444 GCCAGAGCCGGA--GGCAGT
1 GCCAGAGCCGGAGCGGCAGT
* *
10494462 GCCAGACCCAGAGCGGC-G-
1 GCCAGAGCCGGAGCGGCAGT
10494480 GCCAGAGCCGGAGC
1 GCCAGAGCCGGAGC
10494494 TACACTCAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
18 36 0.90
19 1 0.03
20 3 0.08
ACGTcount: A:0.25, C:0.34, G:0.40, T:0.01
Consensus pattern (20 bp):
GCCAGAGCCGGAGCGGCAGT
Found at i:10498627 original size:12 final size:12
Alignment explanation
Indices: 10498595--10498633 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
10498585 TAAAATTAAA
10498595 AAATTAA-AAC-
1 AAATTAAGAACT
10498605 AAATT-AGAACT
1 AAATTAAGAACT
10498616 AAATTAAGAACT
1 AAATTAAGAACT
10498628 AAATTA
1 AAATTA
10498634 TATTAATAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 1 0.04
10 8 0.31
11 5 0.19
12 12 0.46
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.26
Consensus pattern (12 bp):
AAATTAAGAACT
Found at i:10498938 original size:2 final size:2
Alignment explanation
Indices: 10498931--10498969 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
10498921 TCTAGCCACA
10498931 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
10498970 TTTAAGATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:10500587 original size:23 final size:23
Alignment explanation
Indices: 10500561--10500610 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
10500551 ATATATAAAC
10500561 AAATTTTAAAAATATAATATATT
1 AAATTTTAAAAATATAATATATT
10500584 AAATTTTAAAAATATAATATATT
1 AAATTTTAAAAATATAATATATT
10500607 AAAT
1 AAAT
10500611 ACACTAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
AAATTTTAAAAATATAATATATT
Found at i:10500618 original size:25 final size:23
Alignment explanation
Indices: 10500567--10500623 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
10500557 AAACAAATTT
**
10500567 TAAAAATATAATATATTAAATTT
1 TAAAAATATAATATATTAAATAC
10500590 TAAAAATATAATATATTAAATACAC
1 TAAAAATATAATATATTAAAT--AC
10500615 TAAAAATAT
1 TAAAAATAT
10500624 TAAAATAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 21 0.70
25 9 0.30
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (23 bp):
TAAAAATATAATATATTAAATAC
Found at i:10500742 original size:12 final size:11
Alignment explanation
Indices: 10500719--10500804 Score: 59
Period size: 11 Copynumber: 7.7 Consensus size: 11
10500709 GTAAATATTT
10500719 ATAAAATAATA
1 ATAAAATAATA
10500730 ATAAAATTAATA
1 ATAAAA-TAATA
* *
10500742 ATAAAACAAAA
1 ATAAAATAATA
* *
10500753 ATTATATAATA
1 ATAAAATAATA
* *
10500764 TTCAAATAATA
1 ATAAAATAATA
*
10500775 ATATTAA-AATA
1 ATA-AAATAATA
10500786 ATAACAAT-ATA
1 ATAA-AATAATA
*
10500797 ATATAATA
1 ATAAAATA
10500805 GCAAAATAAA
Statistics
Matches: 56, Mismatches: 14, Indels: 10
0.70 0.17 0.12
Matches are distributed among these distances:
10 3 0.05
11 40 0.71
12 13 0.23
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.31
Consensus pattern (11 bp):
ATAAAATAATA
Found at i:10500777 original size:14 final size:14
Alignment explanation
Indices: 10500758--10500789 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
10500748 CAAAAATTAT
*
10500758 ATAATATTCAAATA
1 ATAATATTAAAATA
10500772 ATAATATTAAAATA
1 ATAATATTAAAATA
10500786 ATAA
1 ATAA
10500790 CAATATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAATATTAAAATA
Found at i:10500812 original size:41 final size:42
Alignment explanation
Indices: 10500726--10500818 Score: 102
Period size: 41 Copynumber: 2.2 Consensus size: 42
10500716 TTTATAAAAT
* * *
10500726 AATAATAAAATTAATAATAAAACAAAAATTATATAATATTCA
1 AATAATAATATTAATAATAAAACAAAAATAATATAATATGCA
*
10500768 AATAATAATATTAA-AATAATAAC-AATATAATATAATA-GCAA
1 AATAATAATATTAATAATAA-AACAAAAATAATATAATATGC-A
*
10500809 AATAAAAATA
1 AATAATAATA
10500819 AAACACAAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
40 1 0.02
41 27 0.61
42 16 0.36
ACGTcount: A:0.66, C:0.04, G:0.01, T:0.29
Consensus pattern (42 bp):
AATAATAATATTAATAATAAAACAAAAATAATATAATATGCA
Found at i:10501328 original size:21 final size:21
Alignment explanation
Indices: 10501299--10501339 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
10501289 TGAATGAACT
10501299 GATTAAATTAATAATTTAATC
1 GATTAAATTAATAATTTAATC
* *
10501320 GATTTAATTATTAATTTAAT
1 GATTAAATTAATAATTTAAT
10501340 TTTAAAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (21 bp):
GATTAAATTAATAATTTAATC
Found at i:10504932 original size:23 final size:23
Alignment explanation
Indices: 10504874--10504934 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
10504864 ACTTTTTACT
*
10504874 TAGTTTTAATTTTCCTTTCAATTT
1 TAGTTTTAA-TTTCCTTTCAATTG
* *
10504898 TA-ATTTAGATTTCTTTTCAATTG
1 TAGTTTTA-ATTTCCTTTCAATTG
*
10504921 TAGTTTTTATTTCC
1 TAGTTTTAATTTCC
10504935 ATTTTCTATC
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
23 23 0.79
24 6 0.21
ACGTcount: A:0.21, C:0.11, G:0.07, T:0.61
Consensus pattern (23 bp):
TAGTTTTAATTTCCTTTCAATTG
Found at i:10509594 original size:18 final size:18
Alignment explanation
Indices: 10509571--10509613 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
10509561 TCACAGTAGT
*
10509571 CTTTGCTGATGACGATGC
1 CTTTGCCGATGACGATGC
10509589 CTTTGCCGATGACGATGC
1 CTTTGCCGATGACGATGC
10509607 CTTTGCC
1 CTTTGCC
10509614 ATTTTTCTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.14, C:0.28, G:0.26, T:0.33
Consensus pattern (18 bp):
CTTTGCCGATGACGATGC
Found at i:10510663 original size:34 final size:34
Alignment explanation
Indices: 10510579--10510665 Score: 129
Period size: 34 Copynumber: 2.6 Consensus size: 34
10510569 GTGGAATGCC
10510579 AATAGGCCCTGCTAGGTTAATGACTAGTTCATTG
1 AATAGGCCCTGCTAGGTTAATGACTAGTTCATTG
** * *
10510613 AATAGAACTTGCTAGGTTAATGACTAGTTGATTG
1 AATAGGCCCTGCTAGGTTAATGACTAGTTCATTG
*
10510647 AATAGGCCCTGATAGGTTA
1 AATAGGCCCTGCTAGGTTA
10510666 GTAGTTCTTG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (34 bp):
AATAGGCCCTGCTAGGTTAATGACTAGTTCATTG
Found at i:10512793 original size:30 final size:30
Alignment explanation
Indices: 10512759--10512825 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
10512749 AATCAAAGAT
*
10512759 AGATTCATATTTAGATTCAAATATGTGTGA
1 AGATTCATATTTAAATTCAAATATGTGTGA
10512789 AGATTCATATTTAAATTCAAATATGTGTGA
1 AGATTCATATTTAAATTCAAATATGTGTGA
*
10512819 AGTTTCA
1 AGATTCA
10512826 AATCCAGTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.40
Consensus pattern (30 bp):
AGATTCATATTTAAATTCAAATATGTGTGA
Found at i:10512794 original size:18 final size:18
Alignment explanation
Indices: 10512771--10512828 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 18
10512761 ATTCATATTT
10512771 AGATTCAAATATGTGTGA
1 AGATTCAAATATGTGTGA
10512789 AGATTC--ATAT-T-T-A
1 AGATTCAAATATGTGTGA
10512802 A-ATTCAAATATGTGTGA
1 AGATTCAAATATGTGTGA
*
10512819 AGTTTCAAAT
1 AGATTCAAAT
10512829 CCAGTGGTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
12 4 0.12
13 2 0.06
14 5 0.15
15 2 0.06
16 5 0.15
17 2 0.06
18 13 0.39
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.38
Consensus pattern (18 bp):
AGATTCAAATATGTGTGA
Found at i:10524403 original size:16 final size:16
Alignment explanation
Indices: 10524382--10524414 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
10524372 GTATGAGGGC
10524382 AACTATCCAACGCATG
1 AACTATCCAACGCATG
*
10524398 AACTATCCAATGCATG
1 AACTATCCAACGCATG
10524414 A
1 A
10524415 TCTTGAGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.27, G:0.12, T:0.21
Consensus pattern (16 bp):
AACTATCCAACGCATG
Found at i:10530485 original size:99 final size:99
Alignment explanation
Indices: 10530314--10530498 Score: 316
Period size: 99 Copynumber: 1.9 Consensus size: 99
10530304 CCAAAAACAA
* * *
10530314 GCCATTTCCAAGACCATTTCATATATAAACATTTACACTAATAATGCACACTTTCAAAGCGTCAA
1 GCCATTTCCAAGACCATTTCATACATAAACATTTACACCAATAATGCACACTTTCAAAGCATCAA
*
10530379 GACCTTACCTAAACACACACACACACACACACAT
66 AACCTTACCTAAACACACACACACACACACACAT
*
10530413 GCCATTTCCAAGACCATTTCATACATAAACATTTAGACCAATAATGCACACTTTCAAAGCATCAA
1 GCCATTTCCAAGACCATTTCATACATAAACATTTACACCAATAATGCACACTTTCAAAGCATCAA
*
10530478 AACCTTACTTAAACACACACA
66 AACCTTACCTAAACACACACA
10530499 TGTATATGCC
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
99 80 1.00
ACGTcount: A:0.41, C:0.29, G:0.06, T:0.24
Consensus pattern (99 bp):
GCCATTTCCAAGACCATTTCATACATAAACATTTACACCAATAATGCACACTTTCAAAGCATCAA
AACCTTACCTAAACACACACACACACACACACAT
Found at i:10533556 original size:26 final size:26
Alignment explanation
Indices: 10533525--10533632 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
10533515 TGAAATGCCC
*
10533525 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
10533551 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
10533577 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
10533603 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
10533629 ATCA
1 ATCA
10533633 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:10537797 original size:27 final size:27
Alignment explanation
Indices: 10537744--10537797 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
10537734 TTAAACCACA
**
10537744 TATCTATTCTGGTGGCTTGACCACACT
1 TATCTATTCTGGCAGCTTGACCACACT
*
10537771 TATCTGATTCTGGCAGCTT-ACCGCACT
1 TATCT-ATTCTGGCAGCTTGACCACACT
10537798 ATTTTTGGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.35
Consensus pattern (27 bp):
TATCTATTCTGGCAGCTTGACCACACT
Found at i:10539571 original size:34 final size:35
Alignment explanation
Indices: 10539527--10539592 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 35
10539517 CTTTTTTTAA
* *
10539527 TGTGTTTCGGATGGA-TAGATCTTATGAGCATTGG
1 TGTGTCTCGGATGGATTAGATCTTACGAGCATTGG
*
10539561 TGTGTCTCGGATGGATTAGCTCTTACGAGCAT
1 TGTGTCTCGGATGGATTAGATCTTACGAGCAT
10539593 CTAAAGTGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 14 0.50
35 14 0.50
ACGTcount: A:0.20, C:0.14, G:0.30, T:0.36
Consensus pattern (35 bp):
TGTGTCTCGGATGGATTAGATCTTACGAGCATTGG
Found at i:10545306 original size:46 final size:46
Alignment explanation
Indices: 10545112--10545292 Score: 199
Period size: 46 Copynumber: 3.9 Consensus size: 46
10545102 TGTAACCCGC
* * *
10545112 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC-GGACGCTCGCAT
* *
10545158 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* * **
10545208 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
*
10545251 CCATAAGTGAACTCGGACTCAACTCAACGAGTTGGGACGCTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTC
10545293 AACCATCCTA
Statistics
Matches: 111, Mismatches: 16, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 4 0.04
46 66 0.59
47 31 0.28
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:10549500 original size:51 final size:51
Alignment explanation
Indices: 10549440--10549546 Score: 214
Period size: 51 Copynumber: 2.1 Consensus size: 51
10549430 TATAATTCCC
10549440 TTAGGATATTTAACAGATCTATCAGCTAATTGAATACTCATCCTAGTGGGT
1 TTAGGATATTTAACAGATCTATCAGCTAATTGAATACTCATCCTAGTGGGT
10549491 TTAGGATATTTAACAGATCTATCAGCTAATTGAATACTCATCCTAGTGGGT
1 TTAGGATATTTAACAGATCTATCAGCTAATTGAATACTCATCCTAGTGGGT
10549542 TTAGG
1 TTAGG
10549547 TTCCCCAAGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.36
Consensus pattern (51 bp):
TTAGGATATTTAACAGATCTATCAGCTAATTGAATACTCATCCTAGTGGGT
Found at i:10558806 original size:13 final size:13
Alignment explanation
Indices: 10558788--10558813 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10558778 TGTTCTGGTA
10558788 GTGTATCCATCCT
1 GTGTATCCATCCT
10558801 GTGTATCCATCCT
1 GTGTATCCATCCT
10558814 TATCGAACGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.15, T:0.38
Consensus pattern (13 bp):
GTGTATCCATCCT
Found at i:10566216 original size:35 final size:34
Alignment explanation
Indices: 10566177--10566247 Score: 115
Period size: 35 Copynumber: 2.1 Consensus size: 34
10566167 AGTTCACTCA
*
10566177 AAATCACAATATCTAAGAGCTTACAATAAAATTCG
1 AAATCACAATATCTAAGAGCCTACAATAAAA-TCG
*
10566212 AAATCACAATATTTAAGAGCCTACAATAAAATCG
1 AAATCACAATATCTAAGAGCCTACAATAAAATCG
10566246 AA
1 AA
10566248 GCTAGTTAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
34 5 0.15
35 29 0.85
ACGTcount: A:0.51, C:0.17, G:0.08, T:0.24
Consensus pattern (34 bp):
AAATCACAATATCTAAGAGCCTACAATAAAATCG
Found at i:10573765 original size:21 final size:20
Alignment explanation
Indices: 10573727--10573767 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
10573717 ATGGGGGTAA
10573727 AGGGTGAGAAATAAAAGTTT
1 AGGGTGAGAAATAAAAGTTT
10573747 AGGG-GAGAAAATAAAAAGTTT
1 AGGGTGAG-AAAT-AAAAGTTT
10573768 TGGGAGTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.16
20 8 0.42
21 8 0.42
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.22
Consensus pattern (20 bp):
AGGGTGAGAAATAAAAGTTT
Done.