Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 4 of 186
Found at i:1186273 original size:28 final size:28
Alignment explanation
Indices: 1186209--1186391 Score: 287
Period size: 28 Copynumber: 6.5 Consensus size: 28
1186199 TATATTAAGT
*
1186209 TCGCACACTCAGTGCTATATAATC-AAC
1 TCGCACACTTAGTGCTATATAATCAAAC
1186236 TCGCACACTTAGTGCTATATAATCAAAC
1 TCGCACACTTAGTGCTATATAATCAAAC
*
1186264 TCGCACACTTAGTGCTACATAATCAAAC
1 TCGCACACTTAGTGCTATATAATCAAAC
*
1186292 TTGCACACTTAGTGCTATATAATCAAAC
1 TCGCACACTTAGTGCTATATAATCAAAC
1186320 TCGCACACTTAGTGCTATATAATCAAAC
1 TCGCACACTTAGTGCTATATAATCAAAC
* * *
1186348 TCGCACACTTAGTGCTGTACAATTTAAAC
1 TCGCACACTTAGTGCTATATAA-TCAAAC
*
1186377 CCGCACACTTAGTGC
1 TCGCACACTTAGTGC
1186392 CAATCTCATG
Statistics
Matches: 145, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
27 23 0.16
28 103 0.71
29 19 0.13
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.28
Consensus pattern (28 bp):
TCGCACACTTAGTGCTATATAATCAAAC
Found at i:1190523 original size:19 final size:18
Alignment explanation
Indices: 1190495--1190531 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
1190485 ATATATTGTA
1190495 TTTTTTTCTTTGTTTTTG
1 TTTTTTTCTTTGTTTTTG
1190513 TTTTTTATCTTTGTTTTTG
1 TTTTTT-TCTTTGTTTTTG
1190532 CTTGTTCGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.03, C:0.05, G:0.11, T:0.81
Consensus pattern (18 bp):
TTTTTTTCTTTGTTTTTG
Found at i:1197872 original size:48 final size:48
Alignment explanation
Indices: 1197817--1197943 Score: 218
Period size: 48 Copynumber: 2.6 Consensus size: 48
1197807 AGGTGCCAAA
1197817 ATCATGGCCCGAAGCCAAATCAATGAAGCTCGCATCCGAAGTGCTAAT
1 ATCATGGCCCGAAGCCAAATCAATGAAGCTCGCATCCGAAGTGCTAAT
* * *
1197865 ATCATGGCCTGAAGCCAAATCAATAAAGCTAGCATCCGAAGTGCTAAT
1 ATCATGGCCCGAAGCCAAATCAATGAAGCTCGCATCCGAAGTGCTAAT
*
1197913 ATCATGGCCCGAAGCCAAATTAATGAAGCTC
1 ATCATGGCCCGAAGCCAAATCAATGAAGCTC
1197944 TTAATGACAT
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 72 1.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (48 bp):
ATCATGGCCCGAAGCCAAATCAATGAAGCTCGCATCCGAAGTGCTAAT
Found at i:1214916 original size:85 final size:84
Alignment explanation
Indices: 1214789--1214948 Score: 207
Period size: 85 Copynumber: 1.9 Consensus size: 84
1214779 CATACCAATT
* * * * * *
1214789 CCATATCCCAGATATGGTCTTACATGGGATCTCGTATCGATGCTAATAGCCTAGCTATGGTCTTA
1 CCATATCCCAGATATGGTCTTACACGAGATCTCATATAGATGC-AATAGCCCAGATATGGTCTTA
1214854 CACGA-AGTCTTTTATTGATG
65 CAC-ATAGTCTTTTATTGATG
* *
1214874 CCATATCCCAGATATGGTCTTACACGA-AGTCTCATATAGATGCCATATCCCAGATATGGTCTTA
1 CCATATCCCAGATATGGTCTTACACGAGA-TCTCATATAGATGCAATAGCCCAGATATGGTCTTA
1214938 CACATAGTCTT
65 CACATAGTCTT
1214949 AGTAACCCTA
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
83 1 0.02
84 27 0.42
85 37 0.57
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (84 bp):
CCATATCCCAGATATGGTCTTACACGAGATCTCATATAGATGCAATAGCCCAGATATGGTCTTAC
ACATAGTCTTTTATTGATG
Found at i:1214947 original size:42 final size:42
Alignment explanation
Indices: 1214789--1214940 Score: 180
Period size: 42 Copynumber: 3.6 Consensus size: 42
1214779 CATACCAATT
* * * *
1214789 CCATATCCCAGATATGGTCTTACATG-GGATCTCGTATCGATG
1 CCATATCCCAGATATGGTCTTACACGAAG-TCTCATATAGATG
* * * * ** *
1214831 CTAATAGCCTAGCTATGGTCTTACACGAAGTCTTTTATTGATG
1 C-CATATCCCAGATATGGTCTTACACGAAGTCTCATATAGATG
1214874 CCATATCCCAGATATGGTCTTACACGAAGTCTCATATAGATG
1 CCATATCCCAGATATGGTCTTACACGAAGTCTCATATAGATG
1214916 CCATATCCCAGATATGGTCTTACAC
1 CCATATCCCAGATATGGTCTTACAC
1214941 ATAGTCTTAG
Statistics
Matches: 92, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
42 60 0.65
43 31 0.34
44 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.32
Consensus pattern (42 bp):
CCATATCCCAGATATGGTCTTACACGAAGTCTCATATAGATG
Found at i:1222948 original size:46 final size:46
Alignment explanation
Indices: 1222897--1222989 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
1222887 TTATATTTGA
*
1222897 TTGAAAACTATTGTTATACGTAAATTCAATCAACGGCAAATATTTT
1 TTGAAAACTATTGTTATACGTAAATTCAATCAACGACAAATATTTT
*
1222943 TTGAAAACTATTGTTATACGTAAATTCAATCAATGACAAATATTTT
1 TTGAAAACTATTGTTATACGTAAATTCAATCAACGACAAATATTTT
1222989 T
1 T
1222990 CCCATGTACC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.39
Consensus pattern (46 bp):
TTGAAAACTATTGTTATACGTAAATTCAATCAACGACAAATATTTT
Found at i:1225606 original size:37 final size:37
Alignment explanation
Indices: 1225546--1225623 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
1225536 TATTACGAAA
* *
1225546 TCTTACCCGGACATAATCTCCACACGAAGTTATCGGG
1 TCTTACCCGGACAAAATCTCCACACGAAGTCATCGGG
*
1225583 TCTTACCCGGACAAAAT-TCCCACACGTAGTCATCGGG
1 TCTTACCCGGACAAAATCT-CCACACGAAGTCATCGGG
1225620 TCTT
1 TCTT
1225624 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 1 0.03
37 36 0.97
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.26
Consensus pattern (37 bp):
TCTTACCCGGACAAAATCTCCACACGAAGTCATCGGG
Found at i:1225820 original size:47 final size:47
Alignment explanation
Indices: 1225742--1225897 Score: 231
Period size: 47 Copynumber: 3.3 Consensus size: 47
1225732 CCCTTCGGGA
* * * *
1225742 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACGTTGGCCATTAGGC
* * * *
1225789 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACGTTGGCCATTAGGC
*
1225836 CTTATCACATATATACACTCTCACATTCATCACGTTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACGTTGGCCATTAGGC
1225883 CTTATCACATATATA
1 CTTATCACATATATA
1225898 TATATACACT
Statistics
Matches: 96, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 96 1.00
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACGTTGGCCATTAGGC
Found at i:1229808 original size:27 final size:26
Alignment explanation
Indices: 1229758--1229874 Score: 119
Period size: 27 Copynumber: 4.4 Consensus size: 26
1229748 ACCTTGTAGA
* *
1229758 GTAAAATGA-TCTAATGCCCGTATAGG
1 GTAAAATGACTGTAATACCC-TATAGG
*
1229784 GTAAAATGACCGTAATACCTCTATAGG
1 GTAAAATGACTGTAATACC-CTATAGG
* * *
1229811 GTAAAATGACTGTAATGCCCTTGTAAG
1 GTAAAATGACTGTAATACCC-TATAGG
* *
1229838 GTAAAATGACTGTAATACCCCTTTATG
1 GTAAAATGACTGTAATA-CCCTATAGG
1229865 GTAAAATGAC
1 GTAAAATGAC
1229875 GATTATGGCC
Statistics
Matches: 77, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
26 10 0.13
27 63 0.82
28 4 0.05
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (26 bp):
GTAAAATGACTGTAATACCCTATAGG
Found at i:1229841 original size:54 final size:54
Alignment explanation
Indices: 1229758--1229874 Score: 155
Period size: 54 Copynumber: 2.2 Consensus size: 54
1229748 ACCTTGTAGA
* *
1229758 GTAAAATGA-TCTAATGCCCGTATAGGGTAAAATGACCGTAATACCTCTATAGG
1 GTAAAATGACTCTAATGCCCGTATAAGGTAAAATGACCGTAATACCCCTATAGG
* * * * * *
1229811 GTAAAATGACTGTAATGCCCTTGTAAGGTAAAATGACTGTAATACCCCTTTATG
1 GTAAAATGACTCTAATGCCCGTATAAGGTAAAATGACCGTAATACCCCTATAGG
1229865 GTAAAATGAC
1 GTAAAATGAC
1229875 GATTATGGCC
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
53 9 0.16
54 46 0.84
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (54 bp):
GTAAAATGACTCTAATGCCCGTATAAGGTAAAATGACCGTAATACCCCTATAGG
Found at i:1230267 original size:28 final size:28
Alignment explanation
Indices: 1230222--1230281 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
1230212 GCATTACACT
* *
1230222 ACTGATACTACATTGGGCTTAGGCCCAC
1 ACTGATACTACATAGGGCTAAGGCCCAC
* * *
1230250 ACTGCTACTATATAGGGCTAAGGCCCAG
1 ACTGATACTACATAGGGCTAAGGCCCAC
1230278 ACTG
1 ACTG
1230282 TATGTACTGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (28 bp):
ACTGATACTACATAGGGCTAAGGCCCAC
Found at i:1235599 original size:16 final size:16
Alignment explanation
Indices: 1235578--1235610 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1235568 ACTCACACAC
1235578 TTAGTGCAATAATGAT
1 TTAGTGCAATAATGAT
1235594 TTAGTGCAATAATGAT
1 TTAGTGCAATAATGAT
1235610 T
1 T
1235611 AGCTGAAGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.39
Consensus pattern (16 bp):
TTAGTGCAATAATGAT
Found at i:1237896 original size:23 final size:22
Alignment explanation
Indices: 1237870--1237921 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
1237860 TAATATTTAT
*
1237870 AACATCACAATTTACCTATTCAA
1 AACATCACAATTT-CATATTCAA
*
1237893 AACAT-ACCAATTTCATATTCAC
1 AACATCA-CAATTTCATATTCAA
1237915 AA-ATCAC
1 AACATCAC
1237922 CTAATTGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 3 0.12
22 11 0.44
23 11 0.44
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (22 bp):
AACATCACAATTTCATATTCAA
Found at i:1245084 original size:5 final size:5
Alignment explanation
Indices: 1245074--1245101 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1245064 GATGCCAACC
1245074 ATAAA ATAAA ATAAA ATAAA ATAAA ATA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATA
1245102 TTATTTTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:1250762 original size:27 final size:26
Alignment explanation
Indices: 1250718--1250769 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
1250708 CTCACTGCAA
*
1250718 TCTGGTGGCGTCGCCACATATATCTGT
1 TCTGGTGACGTCGCCACA-ATATCTGT
* *
1250745 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACGTCGCCACAATATCTG
1250770 GCAGTCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (26 bp):
TCTGGTGACGTCGCCACAATATCTGT
Found at i:1268380 original size:191 final size:191
Alignment explanation
Indices: 1268046--1268438 Score: 597
Period size: 191 Copynumber: 2.1 Consensus size: 191
1268036 CTGGTTACTA
* * ** * * *
1268046 TAGACAGTTTGTGAAAGGTTTCTCTATGATTGCAATGCCGATGACGAAGCTATTATAGAAAGATG
1 TAGACGGTTTGTGAAAGGTTTCTCTATGATTGAAACCCCAATGACAAAGCTATTACAGAAAGATG
* *
1268111 TTAAGTTTGAATGGTTAGAAAAGTGCCAGAAAAATTTTGATCAGTTGAAAGCCCTTTTCACCGAA
66 TTAAGCTCGAATGGTTAGAAAAGTGCCAGAAAAATTTTGATCAGTTGAAAGCCCTTTTCACCGAA
* * * *
1268176 GCTCTAATGCTAGTTCAGCTAGAATCGGGGAAAGAATTTTTTATCTATAGTGATGCATCTT
131 GCTCCAATGCTAGTTCAGCCAGAATCGGGGAAAGAATTTGTTATCTATAGTGATACATCTT
1268237 TAGACGGTTTGTGAAAGGTTTCTCTATGATTGAAACCCCAATGACAAAGCTATTACAGAAAGATG
1 TAGACGGTTTGTGAAAGGTTTCTCTATGATTGAAACCCCAATGACAAAGCTATTACAGAAAGATG
* *
1268302 TTAAGCTCGAATGGTTAGAAAAGTGCCAGAAAAGTTTTGATCAGTTGAAAGCCCTTTTGACCGAA
66 TTAAGCTCGAATGGTTAGAAAAGTGCCAGAAAAATTTTGATCAGTTGAAAGCCCTTTTCACCGAA
* * * *
1268367 GCTCCAGTGCTAGTTCAGCCAGAATTGGGTAAAGAATTTGTTATTTATAGTGATACATCTT
131 GCTCCAATGCTAGTTCAGCCAGAATCGGGGAAAGAATTTGTTATCTATAGTGATACATCTT
* *
1268428 TAAATGGTTTG
1 TAGACGGTTTG
1268439 GGTTGCATTT
Statistics
Matches: 181, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
191 181 1.00
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (191 bp):
TAGACGGTTTGTGAAAGGTTTCTCTATGATTGAAACCCCAATGACAAAGCTATTACAGAAAGATG
TTAAGCTCGAATGGTTAGAAAAGTGCCAGAAAAATTTTGATCAGTTGAAAGCCCTTTTCACCGAA
GCTCCAATGCTAGTTCAGCCAGAATCGGGGAAAGAATTTGTTATCTATAGTGATACATCTT
Found at i:1271058 original size:47 final size:47
Alignment explanation
Indices: 1271000--1271575 Score: 259
Period size: 47 Copynumber: 12.5 Consensus size: 47
1270990 ATTCAGCCAA
* *
1271000 GAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1271047 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
* * * * * * *
1271094 GAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
* * * * * * *
1271141 GAAAGTGCATAAATGTGATAAGTCCCGAA-GGGC-ATTTG-TGTCA-GT
1 GAAAGTGTATATATGTGATAAG-GCCTAATGGCCGATGTGATG-AATGT
* * * * * * *
1271186 -AAAGTGCATAAATGTGATAAGTCCCGAA-GGGC-ATTTG-TGTCA-GT
1 GAAAGTGTATATATGTGATAAG-GCCTAATGGCCGATGTGATG-AATGT
* * * * * * *
1271230 -AAAGTGCATAAATGTGATAAGTCCCGAA-GGGC-ATTTG-TGTCA-GT
1 GAAAGTGTATATATGTGATAAG-GCCTAATGGCCGATGTGATG-AATGT
* * * * * * *
1271274 -AAAGTGCATAAATGTGATAAGTCCCGAA-GGGC-ATTTG-TGTCA-GT
1 GAAAGTGTATATATGTGATAAG-GCCTAATGGCCGATGTGATG-AATGT
* * * * * * *
1271318 -AAAGTGCATAAATGTGATAAGTCCCGAA-GGGC-ATTTG-TGTCA-GT
1 GAAAGTGTATATATGTGATAAG-GCCTAATGGCCGATGTGATG-AATGT
* * * * * *
1271362 -AAAGTGCATAAATGTGATAAGTCCCGAAGGGCATTTG-TGTCCGATGAATGT
1 GAAAGTGTATATATGTGATAAG-GCCTAATGGC---CGATGT--GATGAATGT
* *
1271413 GAAAGTGTATATCTGTGATAAGGCCTAATGGCCGATGTGATGGATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
* *
1271460 GAAAGTGTATAAATGTAATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
* * * * * * *
1271507 GAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
* *
1271554 GAAAGTGCATAAATGTGATAAG
1 GAAAGTGTATATATGTGATAAG
1271576 TCCCGAAGGG
Statistics
Matches: 468, Mismatches: 48, Indels: 26
0.86 0.09 0.05
Matches are distributed among these distances:
44 204 0.44
45 6 0.01
46 4 0.01
47 213 0.46
48 7 0.01
49 3 0.01
50 2 0.00
51 11 0.02
52 18 0.04
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.27
Consensus pattern (47 bp):
GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
Found at i:1271194 original size:44 final size:44
Alignment explanation
Indices: 1271142--1271643 Score: 532
Period size: 44 Copynumber: 11.0 Consensus size: 44
1271132 GATGGATGTG
1271142 AAAGTGCATAAATGTGATAAGTCCCGAAGGGCATTTGTGTCAGT
1 AAAGTGCATAAATGTGATAAGTCCCGAAGGGCATTTGTGTCAGT
1271186 AAAGTGCATAAATGTGATAAGTCCCGAAGGGCATTTGTGTCAGT
1 AAAGTGCATAAATGTGATAAGTCCCGAAGGGCATTTGTGTCAGT
1271230 AAAGTGCATAAATGTGATAAGTCCCGAAGGGCATTTGTGTCAGT
1 AAAGTGCATAAATGTGATAAGTCCCGAAGGGCATTTGTGTCAGT
1271274 AAAGTGCATAAATGTGATAAGTCCCGAAGGGCATTTGTGTCAGT
1 AAAGTGCATAAATGTGATAAGTCCCGAAGGGCATTTGTGTCAGT
1271318 AAAGTGCATAAATGTGATAAGTCCCGAAGGGCATTTGTGTCAGT
1 AAAGTGCATAAATGTGATAAGTCCCGAAGGGCATTTGTGTCAGT
1271362 AAAGTGCATAAATGTGATAAGTCCCGAAGGGCATTTGTGTCCGATGAATGT
1 AAAGTGCATAAATGTGATAAGTCCCGAAGGGCATTTGTGT-C-----A-GT
* ** * * * * *
1271413 GAAAGTGTATATCTGTGATAAG-GCCTAATGGCCGATGTGATG-GATGT
1 -AAAGTGCATAAATGTGATAAGTCCCGAA-GGGC-ATTTG-TGTCA-GT
* * * * * * *
1271460 GAAAGTGTATAAATGTAATAAG-GCCTAATGGCCGATGTGATG-AATGT
1 -AAAGTGCATAAATGTGATAAGTCCCGAA-GGGC-ATTTG-TGTCA-GT
* * * ** ** *
1271507 GAAAGTGTATATATGTGA-CAGGGCCG-AGTGGCCA-ACGTGATGGATGT
1 -AAAGTGCATAAATGTGATAAGTCCCGAAG-GG-CATTTGTG-T-CA-GT
1271554 GAAAGTGCATAAATGTGATAAGTCCCGAAGGGCATTTGTGTCAGT
1 -AAAGTGCATAAATGTGATAAGTCCCGAAGGGCATTTGTGTCAGT
1271599 AAAGTGCATAAATGTGATAAGTCCCGAAGGGCATTTGTGTCAGT
1 AAAGTGCATAAATGTGATAAGTCCCGAAGGGCATTTGTGTCAGT
1271643 A
1 A
1271644 CTATATCCGG
Statistics
Matches: 410, Mismatches: 28, Indels: 40
0.86 0.06 0.08
Matches are distributed among these distances:
44 263 0.64
45 5 0.01
46 6 0.01
47 90 0.22
48 10 0.02
49 2 0.00
50 1 0.00
51 6 0.01
52 21 0.05
53 4 0.01
54 2 0.00
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (44 bp):
AAAGTGCATAAATGTGATAAGTCCCGAAGGGCATTTGTGTCAGT
Found at i:1271588 original size:25 final size:25
Alignment explanation
Indices: 1271560--1271632 Score: 68
Period size: 25 Copynumber: 3.2 Consensus size: 25
1271550 ATGTGAAAGT
1271560 GCATAAATGTGATAAGTCCCGAAGG
1 GCATAAATGTGATAAGTCCCGAAGG
* * * *
1271585 GCAT--TTGTG-TCAGT---AAAGT
1 GCATAAATGTGATAAGTCCCGAAGG
1271604 GCATAAATGTGATAAGTCCCGAAGG
1 GCATAAATGTGATAAGTCCCGAAGG
1271629 GCAT
1 GCAT
1271633 TTGTGTCAGT
Statistics
Matches: 34, Mismatches: 8, Indels: 12
0.63 0.15 0.22
Matches are distributed among these distances:
19 7 0.21
21 4 0.12
22 8 0.24
23 4 0.12
25 11 0.32
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (25 bp):
GCATAAATGTGATAAGTCCCGAAGG
Found at i:1271637 original size:23 final size:23
Alignment explanation
Indices: 1271567--1271637 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 23
1271557 AGTGCATAAA
1271567 TGTGATAAGTCCCGAAGGGCATT
1 TGTGATAAGTCCCGAAGGGCATT
* * * *
1271590 TGTG-TCAGT---AAAGTGCATAAA
1 TGTGATAAGTCCCGAAGGGCAT--T
1271611 TGTGATAAGTCCCGAAGGGCATT
1 TGTGATAAGTCCCGAAGGGCATT
1271634 TGTG
1 TGTG
1271638 TCAGTACTAT
Statistics
Matches: 34, Mismatches: 8, Indels: 12
0.63 0.15 0.22
Matches are distributed among these distances:
19 7 0.21
21 4 0.12
22 8 0.24
23 8 0.24
25 7 0.21
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.28
Consensus pattern (23 bp):
TGTGATAAGTCCCGAAGGGCATT
Found at i:1271794 original size:37 final size:37
Alignment explanation
Indices: 1271738--1271816 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
1271728 CCGAGCTCTA
* *
1271738 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
1271775 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
1271812 AAGAC
1 AAGAC
1271817 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:1276168 original size:43 final size:43
Alignment explanation
Indices: 1276120--1276287 Score: 182
Period size: 43 Copynumber: 4.0 Consensus size: 43
1276110 AAGATTTCCA
1276120 ATATGTG-TTCTCGTGTAAGACCACGTCTGGGACATTGGCATCG
1 ATATGTGATT-TCGTGTAAGACCACGTCTGGGACATTGGCATCG
* * * *
1276163 ATATGTGATTACGTGTAAGAGCATGTCTAGGACATTGGCATCG
1 ATATGTGATTTCGTGTAAGACCACGTCTGGGACATTGGCATCG
* * *
1276206 -TATTTGATTT-GTGTAAGACC-CTATCTGGGACAGTGGCATCG
1 ATATGTGATTTCGTGTAAGACCAC-GTCTGGGACATTGGCATCG
* ** * *
1276247 ATATATGATAGCATGTAAGACCATGTCTGGGACATTGGCAT
1 ATATGTGATTTCGTGTAAGACCACGTCTGGGACATTGGCAT
1276288 TGTACAATAT
Statistics
Matches: 102, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
41 25 0.25
42 15 0.15
43 60 0.59
44 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.31
Consensus pattern (43 bp):
ATATGTGATTTCGTGTAAGACCACGTCTGGGACATTGGCATCG
Found at i:1276234 original size:84 final size:84
Alignment explanation
Indices: 1276132--1276287 Score: 226
Period size: 84 Copynumber: 1.9 Consensus size: 84
1276122 ATGTGTTCTC
* * * * *
1276132 GTGTAAGACCACGTCTGGGACATTGGCATCGATATGTGATTA-CGTGTAAGAGCATGTCTAGGAC
1 GTGTAAGACCACATCTGGGACAGTGGCATCGATATATGA-TAGCATGTAAGACCATGTCTAGGAC
1276196 ATTGGCATCGTATTTGATTT
65 ATTGGCATCGTATTTGATTT
*
1276216 GTGTAAGACC-CTATCTGGGACAGTGGCATCGATATATGATAGCATGTAAGACCATGTCTGGGAC
1 GTGTAAGACCAC-ATCTGGGACAGTGGCATCGATATATGATAGCATGTAAGACCATGTCTAGGAC
1276280 ATTGGCAT
65 ATTGGCAT
1276288 TGTACAATAT
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
83 3 0.05
84 61 0.95
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (84 bp):
GTGTAAGACCACATCTGGGACAGTGGCATCGATATATGATAGCATGTAAGACCATGTCTAGGACA
TTGGCATCGTATTTGATTT
Found at i:1278058 original size:13 final size:14
Alignment explanation
Indices: 1278027--1278067 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
1278017 TGTAGTTTTC
1278027 ACATGCCCGTGT-A
1 ACATGCCCGTGTCA
*
1278040 ACATGCCCGTGTCC
1 ACATGCCCGTGTCA
1278054 A-ATG-CCGTGTCA
1 ACATGCCCGTGTCA
1278066 AC
1 AC
1278068 CACACTGCTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 8 0.33
13 15 0.62
14 1 0.04
ACGTcount: A:0.22, C:0.34, G:0.22, T:0.22
Consensus pattern (14 bp):
ACATGCCCGTGTCA
Found at i:1278352 original size:28 final size:28
Alignment explanation
Indices: 1278312--1278368 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
1278302 TATCCATCAA
1278312 TCCAACATCATATTCACATAAAATTAGT
1 TCCAACATCATATTCACATAAAATTAGT
1278340 TCCAACATCATATTCACATAAAATTAGT
1 TCCAACATCATATTCACATAAAATTAGT
1278368 T
1 T
1278369 ATCAATCATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.42, C:0.21, G:0.04, T:0.33
Consensus pattern (28 bp):
TCCAACATCATATTCACATAAAATTAGT
Found at i:1291742 original size:47 final size:49
Alignment explanation
Indices: 1291625--1291752 Score: 181
Period size: 48 Copynumber: 2.7 Consensus size: 49
1291615 ATACGTGTAA
*
1291625 GTGGTGCTAAGTGGATATACCATGATTACACATATTGATACATGTAAAT
1 GTGGTGCTAAGTGGATATACCACGATTACACATATTGATACATGTAAAT
** *
1291674 -TGGTGCTAAGTGGATATACCACGATTACATTTATTGATTCAT-T-AAT
1 GTGGTGCTAAGTGGATATACCACGATTACACATATTGATACATGTAAAT
* *
1291720 GTGGTGCTAAGTGGATATACCACGGTTAAACAT
1 GTGGTGCTAAGTGGATATACCACGATTACACAT
1291753 GTAACGTGGT
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
46 3 0.04
47 29 0.41
48 38 0.54
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (49 bp):
GTGGTGCTAAGTGGATATACCACGATTACACATATTGATACATGTAAAT
Found at i:1291771 original size:38 final size:38
Alignment explanation
Indices: 1291720--1291792 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
1291710 ATTCATTAAT
1291720 GTGGTGCTAAGTGGATATACCACGGTTAAACATGTAAC
1 GTGGTGCTAAGTGGATATACCACGGTTAAACATGTAAC
* *
1291758 GTGGTGCTAAGTGGATATGCCACGGTTATACATGT
1 GTGGTGCTAAGTGGATATACCACGGTTAAACATGT
1291793 TAATTTGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (38 bp):
GTGGTGCTAAGTGGATATACCACGGTTAAACATGTAAC
Found at i:1298300 original size:33 final size:33
Alignment explanation
Indices: 1298257--1298320 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
1298247 GCATGTAGTA
*
1298257 ACAGTCTGGGCCTGAGCCCTATTCAATAACAGT
1 ACAGTCTGGGCCTGAGCCCTATACAATAACAGT
* * *
1298290 ACAGTTTGGGCCTTAGCCCTATACAGTAACA
1 ACAGTCTGGGCCTGAGCCCTATACAATAACA
1298321 ATATGGGCTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (33 bp):
ACAGTCTGGGCCTGAGCCCTATACAATAACAGT
Found at i:1298556 original size:27 final size:26
Alignment explanation
Indices: 1298507--1298565 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
1298497 GATGCCAGAA
*
1298507 ACAGTAAATGTGGCAAAGCCACCAGT
1 ACAGTAAATGTGACAAAGCCACCAGT
* * *
1298533 ATCAGTAATTGTGACATAGTCACCAGT
1 A-CAGTAAATGTGACAAAGCCACCAGT
1298560 ACAGTA
1 ACAGTA
1298566 CTTCCTCTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 6 0.21
27 22 0.79
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.22
Consensus pattern (26 bp):
ACAGTAAATGTGACAAAGCCACCAGT
Found at i:1298820 original size:27 final size:26
Alignment explanation
Indices: 1298702--1298846 Score: 164
Period size: 27 Copynumber: 5.4 Consensus size: 26
1298692 GGCATAATCA
1298702 TCATTTTACCATACAAGGGTATTACGG
1 TCATTTTACCATAC-AGGGTATTACGG
*
1298729 TCATTTTACCATACAGGGGCATTACGG
1 TCATTTTACCATACA-GGGTATTACGG
* **
1298756 TCATTTTACCTTACAAGGGTATTACTA
1 TCATTTTACCATAC-AGGGTATTACGG
*
1298783 TCATTTTACCCTACAGGAGTATTACGG
1 TCATTTTACCATACAGG-GTATTACGG
* * *
1298810 TCATTTTACCCTATAGGGGTATTACAG
1 TCATTTTACCATACA-GGGTATTACGG
*
1298837 TTATTTTACC
1 TCATTTTACC
1298847 TATTTTAGGG
Statistics
Matches: 103, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
26 4 0.04
27 96 0.93
28 3 0.03
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (26 bp):
TCATTTTACCATACAGGGTATTACGG
Found at i:1298843 original size:54 final size:54
Alignment explanation
Indices: 1298702--1298846 Score: 193
Period size: 54 Copynumber: 2.7 Consensus size: 54
1298692 GGCATAATCA
* *
1298702 TCATTTTACCATACAAGGGTATTACGGTCATTTTACCATACAGGGGCATTACGG
1 TCATTTTACCATACAAGGGTATTACAGTCATTTTACCATACAGGAGCATTACGG
* * *
1298756 TCATTTTACCTTACAAGGGTATTACTA-TCATTTTACCCTACAGGAGTATTACGG
1 TCATTTTACCATACAAGGGTATTAC-AGTCATTTTACCATACAGGAGCATTACGG
* * * *
1298810 TCATTTTACCCTATAGGGGTATTACAGTTATTTTACC
1 TCATTTTACCATACAAGGGTATTACAGTCATTTTACC
1298847 TATTTTAGGG
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
53 1 0.01
54 79 0.99
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (54 bp):
TCATTTTACCATACAAGGGTATTACAGTCATTTTACCATACAGGAGCATTACGG
Found at i:1302811 original size:27 final size:27
Alignment explanation
Indices: 1302781--1302948 Score: 185
Period size: 27 Copynumber: 6.2 Consensus size: 27
1302771 TAATCATCAA
* * *
1302781 TTTACCATACATGGGTATTGCGGTCAT
1 TTTACCCTACAAGGGTATTACGGTCAT
* * *
1302808 TTTACCATAC-AGGGCTATTATGGTTAT
1 TTTACCCTACAAGGG-TATTACGGTCAT
* *
1302835 TTTACCCTACAGGGGCATTACGGTCAT
1 TTTACCCTACAAGGGTATTACGGTCAT
*
1302862 TTTACCCTACAAGGGTATTACGGTTAT
1 TTTACCCTACAAGGGTATTACGGTCAT
* * *
1302889 TTTACCCTATAAGGGCATTACGATCAT
1 TTTACCCTACAAGGGTATTACGGTCAT
* * *
1302916 TTTATCCTACAAAGGTATTACGGTTAT
1 TTTACCCTACAAGGGTATTACGGTCAT
1302943 TTTACC
1 TTTACC
1302949 TATTTTGGGG
Statistics
Matches: 116, Mismatches: 23, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
26 3 0.03
27 110 0.95
28 3 0.03
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.37
Consensus pattern (27 bp):
TTTACCCTACAAGGGTATTACGGTCAT
Found at i:1302859 original size:54 final size:53
Alignment explanation
Indices: 1302781--1302948 Score: 212
Period size: 54 Copynumber: 3.1 Consensus size: 53
1302771 TAATCATCAA
* * * * *
1302781 TTTACCATACATGGGTATTGCGGTCATTTTACCATAC-AGGGCTATTATGGTTAT
1 TTTACCCTACAAGGGCATTACGGTCATTTTACC-TACAAGGG-TATTACGGTTAT
*
1302835 TTTACCCTACAGGGGCATTACGGTCATTTTACCCTACAAGGGTATTACGGTTAT
1 TTTACCCTACAAGGGCATTACGGTCATTTTA-CCTACAAGGGTATTACGGTTAT
* * *
1302889 TTTACCCTATAAGGGCATTACGATCATTTTATCCTACAAAGGTATTACGGTTAT
1 TTTACCCTACAAGGGCATTACGGTCATTTTA-CCTACAAGGGTATTACGGTTAT
1302943 TTTACC
1 TTTACC
1302949 TATTTTGGGG
Statistics
Matches: 102, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
54 96 0.94
55 6 0.06
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.37
Consensus pattern (53 bp):
TTTACCCTACAAGGGCATTACGGTCATTTTACCTACAAGGGTATTACGGTTAT
Found at i:1321190 original size:40 final size:40
Alignment explanation
Indices: 1321112--1321335 Score: 283
Period size: 40 Copynumber: 5.5 Consensus size: 40
1321102 ACCCAAGTAT
* *
1321112 CTTCGGGATTTAG-CCGGATATAG-CAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* **
1321151 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
1321191 CTTCGGGACTTAGCCCGGATATAGTCACTGGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
1321231 CTCCGGGACTTAGCCCGGGTATAG-CAACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATGC
* * *
1321274 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATTC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1321314 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
1321336 CATCCGAATA
Statistics
Matches: 161, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
39 12 0.07
40 113 0.70
41 1 0.01
43 35 0.22
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:1321295 original size:83 final size:80
Alignment explanation
Indices: 1321112--1321335 Score: 301
Period size: 83 Copynumber: 2.8 Consensus size: 80
1321102 ACCCAAGTAT
* *
1321112 CTTCGGGATTTAG-CCGGATATAG-CAACTTGCACAAATGCCTTCGGGTCTTAGCCCGGATATAG
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTTGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
**
1321175 TCACTAGCATGAATGC
65 TCACTAGCACAAATGC
* * *
1321191 CTTCGGGACTTAGCCCGGATATAGTCACTGGCACAAATGCCTCCGGGACTTAGCCCGGGTATAG-
1 CTTCGGGACTTAGCCCGGATATAGTCACTTGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
1321255 CAACTACTCGCACAAATGC
66 C-ACTA---GCACAAATGC
* *
1321274 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATTCCTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATATAGTCACTTGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1321336 CATCCGAATA
Statistics
Matches: 127, Mismatches: 12, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
79 13 0.10
80 48 0.38
81 1 0.01
83 65 0.51
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.25
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTTGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
CACTAGCACAAATGC
Found at i:1332787 original size:48 final size:48
Alignment explanation
Indices: 1332731--1333212 Score: 784
Period size: 48 Copynumber: 10.0 Consensus size: 48
1332721 CAAGATAAAT
* * *
1332731 ATATGTATATGTGGTAAATCTGAATGGCTAATGTGAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1332779 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* * *
1332827 ATATATATATGTGGTAAAGCCAAATGGCTAATGTGAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1332875 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* * *
1332923 ATATATATATGTGGTAAAGCCAAATGGCTAATGTGAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1332971 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* * *
1333019 ATATATATATGTGGTAAAGCCAAATGGCTAATGTGAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
** *
1333067 ATATGTATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATAAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
1333115 ATATATATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* * *
1333163 ATATGTATATTTGGTAAAGTCGAATGGCTAATGTGAAATATGTAGGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1333211 AT
1 AT
1333213 GTGTGTATAT
Statistics
Matches: 400, Mismatches: 34, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 400 1.00
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.32
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
Found at i:1333396 original size:37 final size:37
Alignment explanation
Indices: 1333342--1333455 Score: 167
Period size: 37 Copynumber: 3.1 Consensus size: 37
1333332 ACATGAAACT
* *
1333342 TGGAGATATAT-TTCGGGTAAGACCCGATTACTACGTG
1 TGGAGAT-TATGTCCGGGTAAGACCCGATAACTACGTG
*
1333379 TGGAGATTATGTCCGGGTAAGACCCGATGACTACGTG
1 TGGAGATTATGTCCGGGTAAGACCCGATAACTACGTG
* *
1333416 TGGAGATTTTGTCTGGGTAAGACCCGATAACTACGTG
1 TGGAGATTATGTCCGGGTAAGACCCGATAACTACGTG
1333453 TGG
1 TGG
1333456 GGACTATTCG
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
36 3 0.04
37 68 0.96
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.28
Consensus pattern (37 bp):
TGGAGATTATGTCCGGGTAAGACCCGATAACTACGTG
Found at i:1335701 original size:40 final size:40
Alignment explanation
Indices: 1334721--1335692 Score: 1865
Period size: 40 Copynumber: 24.3 Consensus size: 40
1334711 GAGTTATATA
*
1334721 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1334761 TATCCGGGCTAAG-TCCTGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTTCC-GAAGAGCATTCGTGCTAGTGATG
* *
1334801 TATCCGGGCTAAGTTTCGAAGAGCATTCGTGCTAGTGATA
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1334841 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1334881 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1334921 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1334961 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1335001 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1335041 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1335081 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1335121 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1335161 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1335201 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1335241 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1335281 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1335321 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1335361 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1335401 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1335441 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1335481 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1335521 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
*
1335561 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATA
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
* *
1335601 TATCCGAGCTAAGTTCCAAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
*
1335641 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATA
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1335681 TATCCGGGCTAA
1 TATCCGGGCTAA
1335693 ACCTCGAAGG
Statistics
Matches: 918, Mismatches: 12, Indels: 4
0.98 0.01 0.00
Matches are distributed among these distances:
39 2 0.00
40 914 1.00
41 2 0.00
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.27
Consensus pattern (40 bp):
TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
Found at i:1335810 original size:57 final size:57
Alignment explanation
Indices: 1335720--1335887 Score: 219
Period size: 57 Copynumber: 2.9 Consensus size: 57
1335710 GCTGGAGTTA
* * * * *
1335720 TGAGGCACTGTGTGTGCAAGTTCTTCAACCGAGCACTATGTGTGCCAGATCAGTAGT
1 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGTAAT
* **
1335777 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTACGAGATTGGTAAT
1 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGTAAT
* * ** *
1335834 TGAGGCACTATGTGTGTGAGTTCTTTAATCGAGCGTTATGTGTGCGAAATCAGT
1 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGT
1335888 CAGTGGGCAC
Statistics
Matches: 95, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 95 1.00
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.32
Consensus pattern (57 bp):
TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGTAAT
Found at i:1335847 original size:29 final size:29
Alignment explanation
Indices: 1335752--1335849 Score: 101
Period size: 29 Copynumber: 3.4 Consensus size: 29
1335742 CTTCAACCGA
* * *
1335752 GCACTATGTGTGCCAGATCAGTAGTTGAG
1 GCACTATGTGTGCGAGATTAGTAATTGAG
** *
1335781 GCACTATGTGTGCGAG-TTCTTCAATCGA-
1 GCACTATGTGTGCGAGATTAGT-AATTGAG
* *
1335809 GCACTATGTGTACGAGATTGGTAATTGAG
1 GCACTATGTGTGCGAGATTAGTAATTGAG
1335838 GCACTATGTGTG
1 GCACTATGTGTG
1335850 TGAGTTCTTT
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
28 22 0.40
29 33 0.60
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (29 bp):
GCACTATGTGTGCGAGATTAGTAATTGAG
Found at i:1335862 original size:29 final size:29
Alignment explanation
Indices: 1335720--1335880 Score: 114
Period size: 28 Copynumber: 5.7 Consensus size: 29
1335710 GCTGGAGTTA
* * * *
1335720 TGAGGCACTGTGTGTGCAAGTTCTTCAAC
1 TGAGGCACTATGTGTGCGAGTTCTTTAAT
* * * ** *
1335749 CGA-GCACTATGTGTGCCAGATCAGTAGT
1 TGAGGCACTATGTGTGCGAGTTCTTTAAT
*
1335777 TGAGGCACTATGTGTGCGAGTTCTTCAAT
1 TGAGGCACTATGTGTGCGAGTTCTTTAAT
* * **
1335806 CGA-GCACTATGTGTACGAGATT-GGTAAT
1 TGAGGCACTATGTGTGCGAG-TTCTTTAAT
*
1335834 TGAGGCACTATGTGTGTGAGTTCTTTAAT
1 TGAGGCACTATGTGTGCGAGTTCTTTAAT
* **
1335863 CGA-GCGTTATGTGTGCGA
1 TGAGGCACTATGTGTGCGA
1335881 AATCAGTCAG
Statistics
Matches: 98, Mismatches: 30, Indels: 9
0.72 0.22 0.07
Matches are distributed among these distances:
28 53 0.54
29 45 0.46
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.32
Consensus pattern (29 bp):
TGAGGCACTATGTGTGCGAGTTCTTTAAT
Found at i:1336976 original size:49 final size:49
Alignment explanation
Indices: 1336904--1337002 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
1336894 GGTGGAAAAA
*
1336904 AATGTAGACTTGCATGTCGAATTCCCCACTTTAGAGGAAGTGGCCGGCC
1 AATGTAGACTTGCATGTCAAATTCCCCACTTTAGAGGAAGTGGCCGGCC
1336953 AATGTAGACTTGCATGTCAAATTCCCCACTTTAGAGGAAGTGGCCGGCC
1 AATGTAGACTTGCATGTCAAATTCCCCACTTTAGAGGAAGTGGCCGGCC
1337002 A
1 A
1337003 TGATGGTATG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.24
Consensus pattern (49 bp):
AATGTAGACTTGCATGTCAAATTCCCCACTTTAGAGGAAGTGGCCGGCC
Found at i:1338664 original size:48 final size:48
Alignment explanation
Indices: 1338608--1339619 Score: 1556
Period size: 48 Copynumber: 21.0 Consensus size: 48
1338598 CAAGATAAAT
* * * *
1338608 ATATGTATATGTGGTAAATCTGAATGGCTAATGTGAAATATATATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
1338656 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
1338704 ATATATATATGTGGTAAAGCCAAATGGCTAATGTGAAATATATATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* ** *
1338752 ATATGTATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATAAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
1338800 ATATATATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
1338848 ATATATATATGTGGTAAAGCCAAATGGCTAATGTGAAATATATATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* ** *
1338896 ATATGTATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATAAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
1338944 ATATATATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
1338992 ATATATATATGTGGTAAAGCCAAATGGCTAATGTGAAATATATATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* ** *
1339040 ATATGTATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATAAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
1339088 ATATATATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
1339136 ATATATATATGTGGTAAAGCCAAATGGCTAATGTGAAATATATATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* ** *
1339184 ATATGTATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATAAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
1339232 ATATATATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
1339280 ATATATATATGTGGTAAAGCCAAATGGCTAATGTGAAATATATATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* ** *
1339328 ATATGTATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATAAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
1339376 ATATATATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
1339424 ATATATATATGTGGTAAAGCCAAATGGCTAATGTGAAATATATATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* **
1339472 ATATGTATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
1339520 ATATATATATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
1 --ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* * * *
1339570 ATATGTATATTTGGTAAAGTCGAATGGCTAATGTGAAATATGTAGGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1339618 AT
1 AT
1339620 GTGTGTATAT
Statistics
Matches: 872, Mismatches: 90, Indels: 4
0.90 0.09 0.00
Matches are distributed among these distances:
48 828 0.95
50 44 0.05
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.32
Consensus pattern (48 bp):
ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
Found at i:1338868 original size:144 final size:144
Alignment explanation
Indices: 1338608--1339619 Score: 1871
Period size: 144 Copynumber: 7.0 Consensus size: 144
1338598 CAAGATAAAT
* * ** * * *
1338608 ATATGTATATGTGGTAAATCTGAATGGCTAATGTGAAATATATATGAGATATGTATATGTGGTAA
1 ATATGTATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATAAGATATATATATGTGGTAA
*
1338673 AGCCGAATGGCTAATGTGAAATATGTATGAGATATATATATGTGGTAAAGCCAAATGGCTAATGT
66 ATCCGAATGGCTAATGTGAAATATGTATGAGATATATATATGTGGTAAAGCCAAATGGCTAATGT
1338738 GAAATATATATGAG
131 GAAATATATATGAG
1338752 ATATGTATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATAAGATATATATATGTGGTAA
1 ATATGTATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATAAGATATATATATGTGGTAA
1338817 ATCCGAATGGCTAATGTGAAATATGTATGAGATATATATATGTGGTAAAGCCAAATGGCTAATGT
66 ATCCGAATGGCTAATGTGAAATATGTATGAGATATATATATGTGGTAAAGCCAAATGGCTAATGT
1338882 GAAATATATATGAG
131 GAAATATATATGAG
1338896 ATATGTATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATAAGATATATATATGTGGTAA
1 ATATGTATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATAAGATATATATATGTGGTAA
1338961 ATCCGAATGGCTAATGTGAAATATGTATGAGATATATATATGTGGTAAAGCCAAATGGCTAATGT
66 ATCCGAATGGCTAATGTGAAATATGTATGAGATATATATATGTGGTAAAGCCAAATGGCTAATGT
1339026 GAAATATATATGAG
131 GAAATATATATGAG
1339040 ATATGTATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATAAGATATATATATGTGGTAA
1 ATATGTATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATAAGATATATATATGTGGTAA
1339105 ATCCGAATGGCTAATGTGAAATATGTATGAGATATATATATGTGGTAAAGCCAAATGGCTAATGT
66 ATCCGAATGGCTAATGTGAAATATGTATGAGATATATATATGTGGTAAAGCCAAATGGCTAATGT
1339170 GAAATATATATGAG
131 GAAATATATATGAG
1339184 ATATGTATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATAAGATATATATATGTGGTAA
1 ATATGTATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATAAGATATATATATGTGGTAA
1339249 ATCCGAATGGCTAATGTGAAATATGTATGAGATATATATATGTGGTAAAGCCAAATGGCTAATGT
66 ATCCGAATGGCTAATGTGAAATATGTATGAGATATATATATGTGGTAAAGCCAAATGGCTAATGT
1339314 GAAATATATATGAG
131 GAAATATATATGAG
1339328 ATATGTATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATAAGATATATATATGTGGTAA
1 ATATGTATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATAAGATATATATATGTGGTAA
1339393 ATCCGAATGGCTAATGTGAAATATGTATGAGATATATATATGTGGTAAAGCCAAATGGCTAATGT
66 ATCCGAATGGCTAATGTGAAATATGTATGAGATATATATATGTGGTAAAGCCAAATGGCTAATGT
1339458 GAAATATATATGAG
131 GAAATATATATGAG
*
1339472 ATATGTATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATGAGATATATATATATGTGGT
1 ATATGTATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTAT-A-AGATATATATATGTGGT
* * * *
1339537 AAATCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATTTGGTAAAGTCGAATGGCTAAT
64 AAATCCGAATGGCTAATGTGAAATATGTATGAGATATATATATGTGGTAAAGCCAAATGGCTAAT
* *
1339602 GTGAAATATGTAGGAG
129 GTGAAATATATATGAG
1339618 AT
1 AT
1339620 GTGTGTATAT
Statistics
Matches: 851, Mismatches: 15, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
144 757 0.89
145 1 0.00
146 93 0.11
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.32
Consensus pattern (144 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATAAGATATATATATGTGGTAA
ATCCGAATGGCTAATGTGAAATATGTATGAGATATATATATGTGGTAAAGCCAAATGGCTAATGT
GAAATATATATGAG
Found at i:1339810 original size:37 final size:37
Alignment explanation
Indices: 1339760--1339862 Score: 161
Period size: 37 Copynumber: 2.8 Consensus size: 37
1339750 GGAAATATAT
1339760 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* * *
1339797 TCCGGGTAAGACCCGATGAATACGTGTGGAGATTTTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
1339834 TCCAGGTAAGACCCGATAACTACGTGTGG
1 TCCGGGTAAGACCCGATGACTACGTGTGG
1339863 GGACTATTCA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:1342945 original size:40 final size:40
Alignment explanation
Indices: 1342894--1343160 Score: 407
Period size: 40 Copynumber: 6.7 Consensus size: 40
1342884 GCTACTTGCT
1342894 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
1342934 CAAATGCCTTCGGG-CTTAGCCCGG-AATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
1342973 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
1343013 CAAATGCCTTCGGGACTTAGCCTGGATATAGTAACTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1343053 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
1343093 CAAATGCCTTCGGG-CTTAGCCCGG-AATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
1343132 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1343161 CATCCGAATA
Statistics
Matches: 205, Mismatches: 16, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
38 2 0.01
39 68 0.33
40 133 0.65
41 2 0.01
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:1342992 original size:79 final size:79
Alignment explanation
Indices: 1342894--1343160 Score: 473
Period size: 79 Copynumber: 3.4 Consensus size: 79
1342884 GCTACTTGCT
1342894 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1342959 ATTAGTCACTAGCA
66 ATTAGTCACTAGCA
*
1342973 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCTGG
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCGG
* * *
1343038 -ATATAGTAACTCGTA
65 AAT-TAGTCACTAGCA
1343053 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1343118 ATTAGTCACTAGCA
66 ATTAGTCACTAGCA
1343132 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1343161 CATCCGAATA
Statistics
Matches: 177, Mismatches: 8, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
79 103 0.58
80 74 0.42
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
ATTAGTCACTAGCA
Found at i:1351279 original size:79 final size:79
Alignment explanation
Indices: 1351181--1351995 Score: 1621
Period size: 79 Copynumber: 10.3 Consensus size: 79
1351171 GCTACTTGCT
*
1351181 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1351246 ATTAGTCACTAGCA
66 ATTAGTCACTAGCA
1351260 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1351325 ATTAGTCACTAGCA
66 ATTAGTCACTAGCA
1351339 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1351404 ATTAGTCACTAGCA
66 ATTAGTCACTAGCA
1351418 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1351483 ATTAGTCACTAGCA
66 ATTAGTCACTAGCA
1351497 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1351562 ATTAGTCACTAGCA
66 ATTAGTCACTAGCA
1351576 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1351641 ATTAGTCACTAGCA
66 ATTAGTCACTAGCA
1351655 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1351720 ATTAGTCACTAGCA
66 ATTAGTCACTAGCA
1351734 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1351799 ATTAGTCACTAGCA
66 ATTAGTCACTAGCA
1351813 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1351878 ATTAGTCACTAGCA
66 ATTAGTCACTAGCA
1351892 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1351957 ATTAGTCACTAGCA
66 ATTAGTCACTAGCA
1351971 CAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
1351996 TTATCATCCG
Statistics
Matches: 735, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 735 1.00
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
ATTAGTCACTAGCA
Found at i:1354647 original size:21 final size:22
Alignment explanation
Indices: 1354601--1354641 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1354591 TAGTCCTCTA
*
1354601 ATCAATTCTAATCAATTATTCT
1 ATCAATTCTAATCAATAATTCT
*
1354623 ATCAATT-TAATCCATAATT
1 ATCAATTCTAATCAATAATT
1354642 TCATCATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.39, C:0.17, G:0.00, T:0.44
Consensus pattern (22 bp):
ATCAATTCTAATCAATAATTCT
Found at i:1354832 original size:14 final size:14
Alignment explanation
Indices: 1354813--1354840 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1354803 ATTCTCTCTT
1354813 TTTCTTTTCTTTCC
1 TTTCTTTTCTTTCC
1354827 TTTCTTTTCTTTCC
1 TTTCTTTTCTTTCC
1354841 CCAATTTCGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTCTTTTCTTTCC
Found at i:1357874 original size:37 final size:37
Alignment explanation
Indices: 1357824--1357898 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
1357814 CCCGAATGGC
*
1357824 ATTACTAAGAACTCATAGTGACCATACCTTGTAGGGA
1 ATTACTAAAAACTCATAGTGACCATACCTTGTAGGGA
1357861 ATTACTAAAAACTCATAGTGACCATACCTTGTAGGGA
1 ATTACTAAAAACTCATAGTGACCATACCTTGTAGGGA
1357898 A
1 A
1357899 AGCTGTCTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (37 bp):
ATTACTAAAAACTCATAGTGACCATACCTTGTAGGGA
Found at i:1361484 original size:37 final size:39
Alignment explanation
Indices: 1361390--1361486 Score: 119
Period size: 40 Copynumber: 2.5 Consensus size: 39
1361380 CACACCAGAA
1361390 TGGCGACCAACGTCTCATCGGATAGTTCAAAGCAAATAAG
1 TGGCGACCAACGTCTCATCGGATAGTTCAAAGC-AATAAG
** *
1361430 TTACGACCAACGTCTCATCGGCTAAG-TCAAAGC-A-AAG
1 TGGCGACCAACGTCTCATCGGAT-AGTTCAAAGCAATAAG
*
1361467 TGGCGACCAACGCCTCATCG
1 TGGCGACCAACGTCTCATCG
1361487 AATCTATCTA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
37 20 0.40
38 1 0.02
40 27 0.54
41 2 0.04
ACGTcount: A:0.32, C:0.28, G:0.22, T:0.19
Consensus pattern (39 bp):
TGGCGACCAACGTCTCATCGGATAGTTCAAAGCAATAAG
Found at i:1369670 original size:30 final size:30
Alignment explanation
Indices: 1369634--1369693 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
1369624 AAAACAAATG
1369634 TCACCTTAATCATTTTTCTTTCTTCTCCAA
1 TCACCTTAATCATTTTTCTTTCTTCTCCAA
1369664 TCACCTTAATCATTTTTCTTTCTTCTCCAA
1 TCACCTTAATCATTTTTCTTTCTTCTCCAA
1369694 CCTTTCATCC
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:0.20, C:0.30, G:0.00, T:0.50
Consensus pattern (30 bp):
TCACCTTAATCATTTTTCTTTCTTCTCCAA
Found at i:1374458 original size:46 final size:48
Alignment explanation
Indices: 1374370--1374638 Score: 308
Period size: 46 Copynumber: 5.8 Consensus size: 48
1374360 GTTAAGGTGT
* *
1374370 TGATGCCATGTCCCAGACATGGTCTTACACTGACT-ATCATCTCATAAC
1 TGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCA-AGC
* *
1374418 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCAT-ATCTCAAGT
1 TGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCAAGC
* *
1374463 TGATGCCATGTCCCAGACATGGTCTTACACTGACT-ATCATCTCGTAGC
1 TGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTC-AAGC
* *
1374511 TGATG-CATGTCCGAGACAT-GTCTTACACTGGCTTA-CATCTCAAGGC
1 TGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCAA-GC
* * * * *
1374557 CGATG-CATGTCCTAGACAT-GTCTTACACTAGCTC-TCGTCTCAATGT
1 TGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCAA-GC
1374603 TGATGCCATGTCCCAGACATGGTCTTACACTGGCTC
1 TGATGCCATGTCCCAGACATGGTCTTACACTGGCTC
1374639 CCATAATGTG
Statistics
Matches: 190, Mismatches: 21, Indels: 20
0.82 0.09 0.09
Matches are distributed among these distances:
45 6 0.03
46 98 0.52
47 61 0.32
48 25 0.13
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (48 bp):
TGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCAAGC
Found at i:1374528 original size:93 final size:93
Alignment explanation
Indices: 1374368--1374638 Score: 352
Period size: 93 Copynumber: 2.9 Consensus size: 93
1374358 TGGTTAAGGT
* *
1374368 GTTGATGCCATGTCCCAGACATGGTCTTACACTGACTATCATCTCATAACCGATGCATGTCCCAG
1 GTTGATGCCATGTCCCAGACATGGTCTTACACTGACTATCATCTC-TAGCTGATGCATGTCCCAG
*
1374433 ACATGTCTTACACTGGCTCATATCTCAA-
65 ACATGTCTTACACTGGCTCACATCTCAAG
*
1374461 GTTGATGCCATGTCCCAGACATGGTCTTACACTGACTATCATCTCGTAGCTGATGCATGTCCGAG
1 GTTGATGCCATGTCCCAGACATGGTCTTACACTGACTATCATCTC-TAGCTGATGCATGTCCCAG
*
1374526 ACATGTCTTACACTGGCTTACATCTCAAG
65 ACATGTCTTACACTGGCTCACATCTCAAG
** * * * * *
1374555 GCCGATG-CATGTCCTAGACAT-GTCTTACACT-AGCTCTCGTCTCAATGTTGATGCCATGTCCC
1 GTTGATGCCATGTCCCAGACATGGTCTTACACTGA-CTATCATCTCTA-GCTGATG-CATGTCCC
1374617 AGACATGGTCTTACACTGGCTC
63 AGACAT-GTCTTACACTGGCTC
1374639 CCATAATGTG
Statistics
Matches: 158, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
91 2 0.01
92 24 0.15
93 113 0.72
94 19 0.12
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (93 bp):
GTTGATGCCATGTCCCAGACATGGTCTTACACTGACTATCATCTCTAGCTGATGCATGTCCCAGA
CATGTCTTACACTGGCTCACATCTCAAG
Found at i:1374656 original size:140 final size:139
Alignment explanation
Indices: 1374371--1374677 Score: 401
Period size: 140 Copynumber: 2.2 Consensus size: 139
1374361 TTAAGGTGTT
1374371 GATGCCATGTCCCAGACATGGTCTTACACTGACTATCATCTCATAACCGATGCATGTCCCAGACA
1 GATG-CATGTCCCAGACAT-GTCTTACACTGACTATCATCTCATAACCGATGCATGTCCCAGACA
* *
1374436 TGTCTTACACTGGCTCATATCTCAAGTTGATGCCATGTCCCAGACATGGTCTTACACTGACTATC
64 TGTCTTACACTAGCTCATATCTCAAGTTGATGCCATGTCCCAGACATGGTCTTACACTGACTACC
* *
1374501 ATCTCGTAGCT
129 ATATCGTAGCC
* * * *
1374512 GATGCATGTCCGAGACATGTCTTACACTGGCT-TACATCTCA-AGGCCGATGCATGTCCTAGACA
1 GATGCATGTCCCAGACATGTCTTACACTGACTAT-CATCTCATA-ACCGATGCATGTCCCAGACA
* * *
1374575 TGTCTTACACTAGCTC-TCGTCTCAATGTTGATGCCATGTCCCAGACATGGTCTTACACTGGCTC
64 TGTCTTACACTAGCTCAT-ATCTCAA-GTTGATGCCATGTCCCAGACATGGTCTTACACTGACTA
*
1374639 CCATAAT-GTGGCC
127 CCAT-ATCGTAGCC
1374652 GATGCATGTCCCAGACA--TCTTACACT
1 GATGCATGTCCCAGACATGTCTTACACT
1374678 AGCCCACACA
Statistics
Matches: 148, Mismatches: 13, Indels: 13
0.85 0.07 0.07
Matches are distributed among these distances:
138 12 0.08
139 59 0.40
140 72 0.49
141 5 0.03
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.29
Consensus pattern (139 bp):
GATGCATGTCCCAGACATGTCTTACACTGACTATCATCTCATAACCGATGCATGTCCCAGACATG
TCTTACACTAGCTCATATCTCAAGTTGATGCCATGTCCCAGACATGGTCTTACACTGACTACCAT
ATCGTAGCC
Found at i:1385591 original size:24 final size:24
Alignment explanation
Indices: 1385563--1385611 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
1385553 CAAAAGAAAA
*
1385563 TTTGTACTAAAGCGTTTGAAAACT
1 TTTGTACTAAAGCGTGTGAAAACT
*
1385587 TTTGTACTAAAGGGTGTGAAAACT
1 TTTGTACTAAAGCGTGTGAAAACT
1385611 T
1 T
1385612 ACCTTCAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (24 bp):
TTTGTACTAAAGCGTGTGAAAACT
Found at i:1396167 original size:30 final size:30
Alignment explanation
Indices: 1396133--1396197 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
1396123 TGACAAACTT
* *
1396133 TTTTTTGTTCATATTATATTTGACTT-TAAA
1 TTTTTTATTCATATTATATCTGACTTCT-AA
*
1396163 TTTTTTATTCGTATTATATCTGACTTCTAA
1 TTTTTTATTCATATTATATCTGACTTCTAA
1396193 TTTTT
1 TTTTT
1396198 ATTTTTGCTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 30 0.97
31 1 0.03
ACGTcount: A:0.23, C:0.09, G:0.06, T:0.62
Consensus pattern (30 bp):
TTTTTTATTCATATTATATCTGACTTCTAA
Found at i:1396385 original size:54 final size:54
Alignment explanation
Indices: 1396326--1396464 Score: 138
Period size: 54 Copynumber: 2.6 Consensus size: 54
1396316 TTATGTTTGC
*
1396326 TATGTATG-TCTGTTACATATGTTATGAATATGTATGC-CTGTTATGTATGTCTAT
1 TATGTATGTTATG-TACATATGTTATGAATATGTAT-CTCTGTTATGTATGTCTAT
** * * * *
1396380 TATGTATGTTATGTATGTATGTTGTGGATATGTATCTGTGTTATGTATGTGTAT
1 TATGTATGTTATGTACATATGTTATGAATATGTATCTCTGTTATGTATGTCTAT
* * ** *
1396434 TATGTCTATTATGTATGTATGTTGTGAATAT
1 TATGTATGTTATGTACATATGTTATGAATAT
1396465 TAGTGCATGT
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
53 1 0.01
54 69 0.95
55 3 0.04
ACGTcount: A:0.23, C:0.05, G:0.22, T:0.50
Consensus pattern (54 bp):
TATGTATGTTATGTACATATGTTATGAATATGTATCTCTGTTATGTATGTCTAT
Found at i:1396401 original size:13 final size:13
Alignment explanation
Indices: 1396281--1396456 Score: 73
Period size: 13 Copynumber: 13.5 Consensus size: 13
1396271 CTTCAGCAAA
1396281 GTATGTTATGTGTAT
1 GTATGTTA--TGTAT
*
1396296 -TACTGTTATGCAT
1 GTA-TGTTATGTAT
1396309 GT-TGTTAT-TAT
1 GTATGTTATGTAT
* *
1396320 GTTTGCTATGTAT
1 GTATGTTATGTAT
* **
1396333 GTCTGTTACATAT
1 GTATGTTATGTAT
*
1396346 GTTATGAATATGTAT
1 G-TATG-TTATGTAT
**
1396361 GCCTGTTATGTAT
1 GTATGTTATGTAT
*
1396374 G--T-CTAT-TAT
1 GTATGTTATGTAT
1396383 GTATGTTATGTAT
1 GTATGTTATGTAT
*
1396396 GTATGTTGTGGATAT
1 GTATGTTAT-G-TAT
* *
1396411 GTAT-CTGTGTTAT
1 GTATGTTATG-TAT
1396424 GTATGTGTAT-TAT
1 GTATGT-TATGTAT
* *
1396437 GTCTATTATGTAT
1 GTATGTTATGTAT
1396450 GTATGTT
1 GTATGTT
1396457 GTGAATATTA
Statistics
Matches: 121, Mismatches: 25, Indels: 32
0.68 0.14 0.18
Matches are distributed among these distances:
9 4 0.03
10 3 0.02
11 6 0.05
12 17 0.14
13 59 0.49
14 12 0.10
15 20 0.17
ACGTcount: A:0.21, C:0.06, G:0.22, T:0.52
Consensus pattern (13 bp):
GTATGTTATGTAT
Found at i:1396595 original size:28 final size:29
Alignment explanation
Indices: 1396564--1396631 Score: 68
Period size: 28 Copynumber: 2.3 Consensus size: 29
1396554 TATTATTGTT
*
1396564 TATTACTGTATGTCATATATTTTA-TG-TA
1 TATTACTGTATGT-ATATATGTTACTGATA
* *
1396592 TATTATTGTTATGTATGTATGTTACGTGATA
1 TATTACTG-TATGTATATATGTTAC-TGATA
1396623 TATTACTGT
1 TATTACTGT
1396632 TTATTATGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
28 15 0.47
29 5 0.16
30 3 0.09
31 9 0.28
ACGTcount: A:0.26, C:0.06, G:0.15, T:0.53
Consensus pattern (29 bp):
TATTACTGTATGTATATATGTTACTGATA
Found at i:1396600 original size:69 final size:68
Alignment explanation
Indices: 1396572--1396796 Score: 265
Period size: 68 Copynumber: 3.3 Consensus size: 68
1396562 TTTATTACTG
* * * *
1396572 TATGTCATATATTTTATGTATATTATTGTTATGTATGTATGTTACGTGATATATTACTGTTTATT
1 TATGTTATATATGTTATGTATATTATTGTTATGTATGTATGTTATGTGGTATATTACTGTTTATT
1396637 ATG
66 ATG
* * * *
1396640 TATGTTATGTATGTTATGTATATTATTGTTATGTTTGTCTGTTATGTGGTATATTACTATTTATT
1 TATGTTATATATGTTATGTATATTATTGTTATGTATGTATGTTATGTGGTATATTACTGTTTATT
1396705 ATTG
66 A-TG
* * * * * * *
1396709 TATATTATTTATGTTATGTATATTACTATTATGTATGTTTATTATGT-GTATATTATTG-TTATG
1 TATGTTATATATGTTATGTATATTATTGTTATGTATGTATGTTATGTGGTATATTACTGTTTAT-
1396772 TATG
65 TATG
* *
1396776 TATATTATGTATGTTATGTAT
1 TATGTTATATATGTTATGTAT
1396797 GTATGTCATC
Statistics
Matches: 137, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
67 26 0.19
68 69 0.50
69 42 0.31
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (68 bp):
TATGTTATATATGTTATGTATATTATTGTTATGTATGTATGTTATGTGGTATATTACTGTTTATT
ATG
Found at i:1396649 original size:9 final size:9
Alignment explanation
Indices: 1396570--1396802 Score: 74
Period size: 9 Copynumber: 25.3 Consensus size: 9
1396560 TGTTTATTAC
*
1396570 TGTATGTCA
1 TGTATGTTA
* *
1396579 TATATTTTA
1 TGTATGTTA
*
1396588 TGTATATTA
1 TGTATGTTA
1396597 TTGTTATG-TA
1 -TG-TATGTTA
1396607 TGTATGTTA
1 TGTATGTTA
*
1396616 CGTGATATATTA
1 --TG-TATGTTA
* *
1396628 CTGTTTATTA
1 -TGTATGTTA
1396638 TGTATGTTA
1 TGTATGTTA
1396647 TGTATGTTA
1 TGTATGTTA
*
1396656 TGTATATTA
1 TGTATGTTA
1396665 TTGTTATGTT-
1 -TG-TATGTTA
*
1396675 TGTCTGTTA
1 TGTATGTTA
*
1396684 TGTGGTATATTA
1 --T-GTATGTTA
* * *
1396696 CTATTTATTA
1 -TGTATGTTA
*
1396706 TTGTATATTA
1 -TGTATGTTA
*
1396716 TTTATGTTA
1 TGTATGTTA
*
1396725 TGTATATTA
1 TGTATGTTA
*
1396734 -CTA--TTA
1 TGTATGTTA
1396740 TGTATGTTTA
1 TGTATG-TTA
1396750 T-TATG---
1 TGTATGTTA
*
1396755 TGTATATTA
1 TGTATGTTA
1396764 TTGTTATG-TA
1 -TG-TATGTTA
*
1396774 TGTATATTA
1 TGTATGTTA
1396783 TGTATGTTA
1 TGTATGTTA
1396792 TGTATG-TA
1 TGTATGTTA
1396800 TGT
1 TGT
1396803 CATCTTTAGC
Statistics
Matches: 169, Mismatches: 32, Indels: 47
0.68 0.13 0.19
Matches are distributed among these distances:
5 1 0.01
6 6 0.04
7 2 0.01
8 19 0.11
9 79 0.47
10 33 0.20
11 17 0.10
12 12 0.07
ACGTcount: A:0.25, C:0.03, G:0.16, T:0.57
Consensus pattern (9 bp):
TGTATGTTA
Found at i:1396652 original size:13 final size:13
Alignment explanation
Indices: 1396598--1396802 Score: 63
Period size: 13 Copynumber: 15.2 Consensus size: 13
1396588 TGTATATTAT
1396598 TGTTATGTATGTA
1 TGTTATGTATGTA
*
1396611 TGTTACGTGATATATTA
1 TGTTA--TG-TAT-GTA
1396628 CTGTTTAT-TATGTA
1 -TG-TTATGTATGTA
1396642 TGTTATGTATGTTA
1 TGTTATGTATG-TA
1396656 TG-TA--TAT-TA
1 TGTTATGTATGTA
* *
1396665 TTGTTATGTTTGTC
1 -TGTTATGTATGTA
*
1396679 TGTTATGT-GGTA
1 TGTTATGTATGTA
* *
1396691 TATTACTATTTAT-TA
1 T-GT--TATGTATGTA
*
1396706 TTGTATAT-TATTTA
1 -TGT-TATGTATGTA
*
1396720 TGTTATGTATATTA
1 TGTTATGTAT-GTA
* *
1396734 CTATTATGTATGTT
1 -TGTTATGTATGTA
*
1396748 TATTATG--TGTA
1 TGTTATGTATGTA
*
1396759 TATTATTGTTATGTA
1 TGTTA-TG-TATGTA
1396774 TGTATAT-TATGTA
1 TGT-TATGTATGTA
1396787 TGTTATGTATGTA
1 TGTTATGTATGTA
1396800 TGT
1 TGT
1396803 CATCTTTAGC
Statistics
Matches: 148, Mismatches: 16, Indels: 56
0.67 0.07 0.25
Matches are distributed among these distances:
9 2 0.01
10 2 0.01
11 13 0.09
12 15 0.10
13 58 0.39
14 16 0.11
15 28 0.19
16 6 0.04
17 3 0.02
18 2 0.01
19 3 0.02
ACGTcount: A:0.24, C:0.02, G:0.17, T:0.57
Consensus pattern (13 bp):
TGTTATGTATGTA
Found at i:1396690 original size:137 final size:135
Alignment explanation
Indices: 1396498--1396796 Score: 377
Period size: 137 Copynumber: 2.2 Consensus size: 135
1396488 GGTATATTAC
* * *
1396498 TATTAAGTATATTAT-TAT-TTATGTATATGATTGTTATGTATGTATGTAATTTGGTATATTATT
1 TATTATGTATATTATGTATGTTATGTATATGATTGTTATGTATGTATGTAATGTGGTATATTACT
* * * * * *
1396561 GTTTATTACTGTATGTCATATATTTTATGTATATTATTGTTATGTATGTATGTTACGTGATATAT
66 ATTTATTACTGTATATCATATATGTTATGTATATTACTATTATGTATGTATATTACGTG-TATAT
1396626 TACTGTT
130 TACTG-T
* * * * *
1396633 TATTATGTATGTTATGTATGTTATGTATATTATTGTTATGTTTGTCTGTTATGTGGTATATTACT
1 TATTATGTATATTATGTATGTTATGTATATGATTGTTATGTATGTATGTAATGTGGTATATTACT
* * * * *
1396698 ATTTATTATTGTATATTATTTATGTTATGTATATTACTATTATGTATGTTTATTATGTGTATATT
66 ATTTATTACTGTATATCATATATGTTATGTATATTACTATTATGTATGTATATTACGTGTATATT
*
1396763 ATTGT
131 ACTGT
1396768 TATGTATGTATATTATGTATGTTATGTAT
1 TAT-TATGTATATTATGTATGTTATGTAT
1396797 GTATGTCATC
Statistics
Matches: 140, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
135 17 0.12
136 36 0.26
137 87 0.62
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (135 bp):
TATTATGTATATTATGTATGTTATGTATATGATTGTTATGTATGTATGTAATGTGGTATATTACT
ATTTATTACTGTATATCATATATGTTATGTATATTACTATTATGTATGTATATTACGTGTATATT
ACTGT
Found at i:1396750 original size:30 final size:30
Alignment explanation
Indices: 1396723--1396783 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
1396713 TTATTTATGT
1396723 TATGTATATTACTATTATGTATGTTTATTA
1 TATGTATATTACTATTATGTATGTTTATTA
* * * *
1396753 TGTGTATATTATTGTTATGTATGTATATTA
1 TATGTATATTACTATTATGTATGTTTATTA
1396783 T
1 T
1396784 GTATGTTATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.02, G:0.13, T:0.57
Consensus pattern (30 bp):
TATGTATATTACTATTATGTATGTTTATTA
Found at i:1396843 original size:13 final size:13
Alignment explanation
Indices: 1396825--1396849 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1396815 TATTTAAAAT
1396825 ATGTATGTATATC
1 ATGTATGTATATC
1396838 ATGTATGTATAT
1 ATGTATGTATAT
1396850 TACAGTTTAT
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:0.32, C:0.04, G:0.16, T:0.48
Consensus pattern (13 bp):
ATGTATGTATATC
Found at i:1398374 original size:34 final size:35
Alignment explanation
Indices: 1398329--1398396 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 35
1398319 TTTGTCTGGA
1398329 TGGATGCTTTCTGAAGGGAAGATTCAA-GGTGAAG
1 TGGATGCTTTCTGAAGGGAAGATTCAAGGGTGAAG
*
1398363 TGGATGTTTTCTGAAGGGAAGATTCAAGGGTGAA
1 TGGATGCTTTCTGAAGGGAAGATTCAAGGGTGAA
1398397 CTTCTGTGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 26 0.81
35 6 0.19
ACGTcount: A:0.29, C:0.07, G:0.35, T:0.28
Consensus pattern (35 bp):
TGGATGCTTTCTGAAGGGAAGATTCAAGGGTGAAG
Found at i:1400957 original size:20 final size:20
Alignment explanation
Indices: 1400932--1401008 Score: 66
Period size: 20 Copynumber: 3.9 Consensus size: 20
1400922 ACAGGATTGT
1400932 ACTTCGATGCCTCTGTTTGC
1 ACTTCGATGCCTCTGTTTGC
* * * *
1400952 ACTTCGGTGCCCCTGATTGA
1 ACTTCGATGCCTCTGTTTGC
* ** *
1400972 ACATTTG-TGCCTCTGCCTAC
1 AC-TTCGATGCCTCTGTTTGC
1400992 ACTTCGATGCCTCTGTT
1 ACTTCGATGCCTCTGTT
1401009 ACGCATCTTT
Statistics
Matches: 42, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
19 3 0.07
20 36 0.86
21 3 0.07
ACGTcount: A:0.13, C:0.31, G:0.19, T:0.36
Consensus pattern (20 bp):
ACTTCGATGCCTCTGTTTGC
Found at i:1401451 original size:13 final size:13
Alignment explanation
Indices: 1401435--1401463 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1401425 AAATATTTAG
1401435 ATGAAATGCTTAT
1 ATGAAATGCTTAT
1401448 ATGAAATGCTTAT
1 ATGAAATGCTTAT
1401461 ATG
1 ATG
1401464 GAATTATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (13 bp):
ATGAAATGCTTAT
Found at i:1406501 original size:24 final size:24
Alignment explanation
Indices: 1406473--1406519 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1406463 TTCATGCAAA
*
1406473 ACATGTTTAATTTG-AGAACTACAG
1 ACATGTTTAACTTGTAGAA-TACAG
1406497 ACATGTTTAACTTGTAGAATACA
1 ACATGTTTAACTTGTAGAATACA
1406520 CCTCCACCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (24 bp):
ACATGTTTAACTTGTAGAATACAG
Found at i:1423161 original size:14 final size:14
Alignment explanation
Indices: 1423142--1423177 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1423132 CAAGAAAGTT
1423142 TATGCAAATGGATG
1 TATGCAAATGGATG
*
1423156 TATGCAAATGTATG
1 TATGCAAATGGATG
*
1423170 AATGCAAA
1 TATGCAAA
1423178 AGCACCAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (14 bp):
TATGCAAATGGATG
Found at i:1423797 original size:60 final size:60
Alignment explanation
Indices: 1423683--1423857 Score: 189
Period size: 60 Copynumber: 2.9 Consensus size: 60
1423673 CATGTATCCT
* * * *
1423683 ATAACACACGTCCATGTGGTATCCCTAGA--CCCCAAATTAGTTACACGG-TCGTGTGTCCC
1 ATAACACACGCCCATGTGGAAGCCCTA-ATTGCCCAAATTAGTTACACGGCT-GTGTGTCCC
* * *
1423742 GA-AGCACACGCCCATGTGGGAA-CCCTAATTTCCCAAATTAGTTACACGGCTGTGTGTCTC
1 -ATAACACACGCCCATGT-GGAAGCCCTAATTGCCCAAATTAGTTACACGGCTGTGTGTCCC
* * *
1423802 ATAACACACGCCCATGTGGAAGCCTTAATTGCCCAAATCAGTCACACGGCTGTGTG
1 ATAACACACGCCCATGTGGAAGCCCTAATTGCCCAAATTAGTTACACGGCTGTGTG
1423858 GTTTCAGAAA
Statistics
Matches: 99, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
58 1 0.01
59 23 0.23
60 74 0.75
61 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (60 bp):
ATAACACACGCCCATGTGGAAGCCCTAATTGCCCAAATTAGTTACACGGCTGTGTGTCCC
Found at i:1428004 original size:13 final size:12
Alignment explanation
Indices: 1427974--1428012 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1427964 CATGCAAAAG
**
1427974 AAAAATAACCAT
1 AAAAATAATAAT
1427986 AAAAATAATAAT
1 AAAAATAATAAT
1427998 AATAAATAATAAT
1 AA-AAATAATAAT
1428011 AA
1 AA
1428013 GAAAAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAAATAATAAT
Found at i:1428660 original size:46 final size:46
Alignment explanation
Indices: 1428593--1428686 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
1428583 TGGGTATGTG
1428593 CAAAATGGGTGGCAAATTGGCCTTGCAAATGGCCTATTTTTGTCCA
1 CAAAATGGGTGGCAAATTGGCCTTGCAAATGGCCTATTTTTGTCCA
1428639 CAAAATGGGTGGCAAATTGGCCTTGCAAATGGCCTATTTTTGTCCA
1 CAAAATGGGTGGCAAATTGGCCTTGCAAATGGCCTATTTTTGTCCA
1428685 CA
1 CA
1428687 CGAGTAGAGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (46 bp):
CAAAATGGGTGGCAAATTGGCCTTGCAAATGGCCTATTTTTGTCCA
Found at i:1449794 original size:76 final size:76
Alignment explanation
Indices: 1449668--1449972 Score: 592
Period size: 76 Copynumber: 4.0 Consensus size: 76
1449658 CACCATTCAC
1449668 AAGCTTGAGGGAGCTTCGGTTTTGATTTTGTTTTGCATTTAAGTCCATTTCTCAATTATTTTCAT
1 AAGCTTGAGGGAGCTTCGGTTTTGATTTTGTTTTGCATTTAAGTCCATTTCTCAATTATTTTCAT
1449733 GATTTTTATGT
66 GATTTTTATGT
1449744 AAGCTTGAGGGAGCTTCGGTTTTGATTTTGTTTTGCATTTAAGTCCATTTCTCAATTATTTTCAT
1 AAGCTTGAGGGAGCTTCGGTTTTGATTTTGTTTTGCATTTAAGTCCATTTCTCAATTATTTTCAT
1449809 GATTTTTATGT
66 GATTTTTATGT
1449820 AAGCTTGAGGGAGCTTCGGTTTTGATTTTGTTTTGCATTTAAGTCCATTTCTCAATTATTTTCAT
1 AAGCTTGAGGGAGCTTCGGTTTTGATTTTGTTTTGCATTTAAGTCCATTTCTCAATTATTTTCAT
1449885 GATTTTTATGT
66 GATTTTTATGT
*
1449896 AAGCTTGAGGGAGCTTCGGTTTTGATTTTGTTTTGCATTTAAGTCCATTTCTGAATTATTTTTCA
1 AAGCTTGAGGGAGCTTCGGTTTTGATTTTGTTTTGCATTTAAGTCCATTTCTCAATTA-TTTTCA
1449961 TGATTTTTATGT
65 TGATTTTTATGT
1449973 TCTTGAGACA
Statistics
Matches: 227, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
76 209 0.92
77 18 0.08
ACGTcount: A:0.20, C:0.11, G:0.19, T:0.50
Consensus pattern (76 bp):
AAGCTTGAGGGAGCTTCGGTTTTGATTTTGTTTTGCATTTAAGTCCATTTCTCAATTATTTTCAT
GATTTTTATGT
Found at i:1451225 original size:37 final size:37
Alignment explanation
Indices: 1451175--1451246 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
1451165 ATGAAACGAA
*
1451175 TAAGACCATAGTTGAAAGACACTATAGCAGTATACAG
1 TAAGACCATAGTTGAAAGAAACTATAGCAGTATACAG
* * *
1451212 TAAGACTATAGTTGAAAGAAACTATGGCATTATAC
1 TAAGACCATAGTTGAAAGAAACTATAGCAGTATAC
1451247 CGGAAATGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (37 bp):
TAAGACCATAGTTGAAAGAAACTATAGCAGTATACAG
Found at i:1451306 original size:45 final size:45
Alignment explanation
Indices: 1451257--1451355 Score: 119
Period size: 45 Copynumber: 2.2 Consensus size: 45
1451247 CGGAAATGAG
* *** *
1451257 TAAGACCATAGCTGAAAGATGTTATGGCATCATGATTCTA-AAGAA
1 TAAGACCATAGCTAAAAGACAATATGGCATCATGAATC-AGAAGAA
* *
1451302 TAAGACTATAGCTAAAAGGCAATATGGCATCATGAATCAGAAGAA
1 TAAGACCATAGCTAAAAGACAATATGGCATCATGAATCAGAAGAA
1451347 TAAGACCAT
1 TAAGACCAT
1451356 GATTGGAAGA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
44 1 0.02
45 44 0.98
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.23
Consensus pattern (45 bp):
TAAGACCATAGCTAAAAGACAATATGGCATCATGAATCAGAAGAA
Found at i:1457412 original size:48 final size:48
Alignment explanation
Indices: 1457323--1457416 Score: 129
Period size: 48 Copynumber: 2.0 Consensus size: 48
1457313 TTTCTTGGCT
* * *
1457323 TAAAAACGCCTAAGTCAGCCTAACTTCCACCGATAATGGATTCAACCG
1 TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
1457371 TAAAAACGCCTAAGTCAG-CTCAAC-TCGCAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAGTCAGCCT-AACTTC-CAACAATAAAGGATTCAAC
1457417 AGAATTCCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
47 4 0.10
48 37 0.90
ACGTcount: A:0.39, C:0.28, G:0.14, T:0.19
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
Found at i:1464873 original size:20 final size:19
Alignment explanation
Indices: 1464848--1464885 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1464838 TTAAAAAGGT
*
1464848 AAATAAAGATAAAAGTAAAC
1 AAATAAAAAT-AAAGTAAAC
1464868 AAATAAAAATAAAGTAAA
1 AAATAAAAATAAAGTAAA
1464886 GTCTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.16
Consensus pattern (19 bp):
AAATAAAAATAAAGTAAAC
Found at i:1469924 original size:444 final size:444
Alignment explanation
Indices: 1469095--1469981 Score: 1756
Period size: 444 Copynumber: 2.0 Consensus size: 444
1469085 GCAATAACAA
1469095 CAACTTTCAATACATGTTAATCAAGTCAACATGCTTTCAGGTATAAAACACATTAATAAAATATA
1 CAACTTTCAATACATGTTAATCAAGTCAACATGCTTTCAGGTATAAAACACATTAATAAAATATA
*
1469160 AAATCATTTTCGAGTCTTATATGAGCTTATGAAAGCTCTTTTACTAACCTGAGGTCGGATAAGAA
66 AAATCATTTTCAAGTCTTATATGAGCTTATGAAAGCTCTTTTACTAACCTGAGGTCGGATAAGAA
1469225 CTTAATTGAAAAGCTTTCAAAACTTGCAAGTTGATGTCACCACATTAGAGTTTTCTTGTCATGAC
131 CTTAATTGAAAAGCTTTCAAAACTTGCAAGTTGATGTCACCACATTAGAGTTTTCTTGTCATGAC
1469290 ATCATCTGTCAATGGGTTACTTTACGACTTTAAAAGTCTCAACTTTATAACGCCACTCACTGTCG
196 ATCATCTGTCAATGGGTTACTTTACGACTTTAAAAGTCTCAACTTTATAACGCCACTCACTGTCG
1469355 ATCTATGTCACAATATTGGGTACAGATGGTCGTGACATCACCCTTGTTTTGGTAAAAGTCCCATT
261 ATCTATGTCACAATATTGGGTACAGATGGTCGTGACATCACCCTTGTTTTGGTAAAAGTCCCATT
1469420 TAGTAAAATTTTCATGCATCCAATGCCAGTATTACCAATTCAAACTCATGCCACTTTACGCCAAA
326 TAGTAAAATTTTCATGCATCCAATGCCAGTATTACCAATTCAAACTCATGCCACTTTACGCCAAA
1469485 TCAAACCTATAACACCTTTGAAGACAATCATACTAATGGCATAAAAACTCATAG
391 TCAAACCTATAACACCTTTGAAGACAATCATACTAATGGCATAAAAACTCATAG
1469539 CAACTTTCAATACATGTTAATCAAGTCAACATGCTTTCAGGTATAAAACACATTAATAAAATATA
1 CAACTTTCAATACATGTTAATCAAGTCAACATGCTTTCAGGTATAAAACACATTAATAAAATATA
1469604 AAATCATTTTCAAGTCTTATATGAGCTTATGAAAGCTCTTTTACTAACCTGAGGTCGGATAAGAA
66 AAATCATTTTCAAGTCTTATATGAGCTTATGAAAGCTCTTTTACTAACCTGAGGTCGGATAAGAA
1469669 CTTAATTGAAAAGCTTTCAAAACTTGCAAGTTGATGTCACCACATTAGAGTTTTCTTGTCATGAC
131 CTTAATTGAAAAGCTTTCAAAACTTGCAAGTTGATGTCACCACATTAGAGTTTTCTTGTCATGAC
1469734 ATCATCTGTCAATGGGTTACTTTACGACTTTAAAAGTCTCAACTTTATAACGCCACTCACTGTCG
196 ATCATCTGTCAATGGGTTACTTTACGACTTTAAAAGTCTCAACTTTATAACGCCACTCACTGTCG
1469799 ATCTATGTCACAATATTGGGTACAGATGGTCGTGACATCACCCTTGTTTTGGTAAAAGTCCCATT
261 ATCTATGTCACAATATTGGGTACAGATGGTCGTGACATCACCCTTGTTTTGGTAAAAGTCCCATT
*
1469864 TGGTAAAATTTTCATGCATCCAATGCCAGTATTACCAATTCAAACTCATGCCACTTTACGCCAAA
326 TAGTAAAATTTTCATGCATCCAATGCCAGTATTACCAATTCAAACTCATGCCACTTTACGCCAAA
1469929 TCAAACCTATAACACCTTTGAAGACAATCATACTAATGGCATAAAAACTCATA
391 TCAAACCTATAACACCTTTGAAGACAATCATACTAATGGCATAAAAACTCATA
1469982 ACCAAAACCT
Statistics
Matches: 441, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
444 441 1.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (444 bp):
CAACTTTCAATACATGTTAATCAAGTCAACATGCTTTCAGGTATAAAACACATTAATAAAATATA
AAATCATTTTCAAGTCTTATATGAGCTTATGAAAGCTCTTTTACTAACCTGAGGTCGGATAAGAA
CTTAATTGAAAAGCTTTCAAAACTTGCAAGTTGATGTCACCACATTAGAGTTTTCTTGTCATGAC
ATCATCTGTCAATGGGTTACTTTACGACTTTAAAAGTCTCAACTTTATAACGCCACTCACTGTCG
ATCTATGTCACAATATTGGGTACAGATGGTCGTGACATCACCCTTGTTTTGGTAAAAGTCCCATT
TAGTAAAATTTTCATGCATCCAATGCCAGTATTACCAATTCAAACTCATGCCACTTTACGCCAAA
TCAAACCTATAACACCTTTGAAGACAATCATACTAATGGCATAAAAACTCATAG
Found at i:1473129 original size:39 final size:42
Alignment explanation
Indices: 1473064--1473141 Score: 108
Period size: 39 Copynumber: 1.9 Consensus size: 42
1473054 ACTGTTCTCC
* * *
1473064 CCCCCAAATTTTTTTGTCGTTGTTTTTTTTTCC-TCTTTCTT
1 CCCCCAAATTTTTTTGTCATTCTTTTTTTTCCCTTCTTTCTT
1473105 CCCCC-AA-TTTTTTGTCATTCTTTTTTTTCCCTTCTTT
1 CCCCCAAATTTTTTTGTCATTCTTTTTTTTCCCTTCTTT
1473142 ATTCTTCTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 21 0.64
40 7 0.21
41 5 0.15
ACGTcount: A:0.08, C:0.27, G:0.05, T:0.60
Consensus pattern (42 bp):
CCCCCAAATTTTTTTGTCATTCTTTTTTTTCCCTTCTTTCTT
Found at i:1477351 original size:73 final size:73
Alignment explanation
Indices: 1477266--1477403 Score: 222
Period size: 73 Copynumber: 1.9 Consensus size: 73
1477256 CTTTATTAAC
* *
1477266 GGTATCGATACTTTTTATTTTTTCTCAATTTTCCTAAAACTTCGAAACTCAAATTGGTATCGATA
1 GGTATCGATACTTTTGATTTTTGCTCAATTTTCCTAAAACTTCGAAACTCAAATTGGTATCGATA
1477331 CCAGGCAA
66 CCAGGCAA
* * * *
1477339 GGTATCGATACTTTTGATTTTTGCTTAATTTTTCTAAAACTTCTAAGCTCAAATTGGTATCGATA
1 GGTATCGATACTTTTGATTTTTGCTCAATTTTCCTAAAACTTCGAAACTCAAATTGGTATCGATA
1477404 TATAGGAGAT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 59 1.00
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (73 bp):
GGTATCGATACTTTTGATTTTTGCTCAATTTTCCTAAAACTTCGAAACTCAAATTGGTATCGATA
CCAGGCAA
Found at i:1480308 original size:22 final size:22
Alignment explanation
Indices: 1480266--1480311 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1480256 ATTAAAATAT
*
1480266 TAATTTATAATCTCTTGATTTA
1 TAATTTATAATCTATTGATTTA
*
1480288 TAATTTATAATTTAATT-ATTTA
1 TAATTTATAATCT-ATTGATTTA
1480310 TA
1 TA
1480312 GAGATGCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (22 bp):
TAATTTATAATCTATTGATTTA
Found at i:1483114 original size:54 final size:53
Alignment explanation
Indices: 1483032--1483147 Score: 128
Period size: 53 Copynumber: 2.2 Consensus size: 53
1483022 GCGTATGTTT
** * *
1483032 AGACCGTGTAACTCTCTTAGTTGAGTCACACGAGT-GTGTGTCAAGCCGTGTGCC
1 AGACCGTGTAACTCTCTTACATGAGTCACA-G-GTCGTGTGTCAAGCCATGTGAC
* *
1483086 AGACCGTGTAACTCT-TTAACATGGGTCACAGGTCGTGTGTCAGGCCATGTGAC
1 AGACCGTGTAACTCTCTT-ACATGAGTCACAGGTCGTGTGTCAAGCCATGTGAC
*
1483139 AGATCGTGT
1 AGACCGTGT
1483148 GAGCCATTGT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
52 2 0.04
53 27 0.51
54 24 0.45
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (53 bp):
AGACCGTGTAACTCTCTTACATGAGTCACAGGTCGTGTGTCAAGCCATGTGAC
Found at i:1488135 original size:43 final size:43
Alignment explanation
Indices: 1488081--1488416 Score: 249
Period size: 43 Copynumber: 7.7 Consensus size: 43
1488071 GACGAAGGGC
*
1488081 CTTAACCCCCTAAGCAGTAGAGTAACAGGCTGAATTTACAGAT
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGAT
* * * * **
1488124 CTTAGCCCCCTAAGCAGTAAGG-AA-AGAGATCGAA--GACGAAGGGC
1 CTTAACCCCCTAAGCAGTAGGGTAACAG-GCT-GAATTTAC--A-GAT
*
1488168 CTTAACCCCCTAAGCAGTAGGGTAACAAGCTGAATTTACAGAT
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGAT
* * * * * **
1488211 CTTAGCTCCCTAAGCAGTAGGGAAACA-GATCGAA--GACGAAGGGC
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCT-GAATTTAC--A-GAT
*
1488255 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAATTTACAGAT
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGAT
* * * * ** **
1488298 CTTAACGCCCTAAGCAGTAGGGAAACA-GATCAA-AGACGAAGGGC
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAATTTAC--A-GAT
*
1488342 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAAAT
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGAT
* * *
1488385 CTTAACCCCCTAAGTAGCAAGGTAACAGGCTG
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTG
1488417 GAAATCAAAT
Statistics
Matches: 223, Mismatches: 49, Indels: 42
0.71 0.16 0.13
Matches are distributed among these distances:
41 8 0.04
42 10 0.04
43 108 0.48
44 80 0.36
45 10 0.04
46 7 0.03
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.18
Consensus pattern (43 bp):
CTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGAT
Found at i:1488171 original size:87 final size:87
Alignment explanation
Indices: 1488060--1488398 Score: 579
Period size: 87 Copynumber: 3.9 Consensus size: 87
1488050 AGAATGGTGT
*
1488060 AACAGATCGAAGACGAAGGGCCTTAACCCCCTAAGCAGTAGAGTAACAGGCTGAATTTACAGATC
1 AACAGATCGAAGACGAAGGGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATC
* *
1488125 TTAGCCCCCTAAGCAGTAAGGA
66 TTAACCCCCTAAGCAGTAGGGA
* *
1488147 AAGAGATCGAAGACGAAGGGCCTTAACCCCCTAAGCAGTAGGGTAACAAGCTGAATTTACAGATC
1 AACAGATCGAAGACGAAGGGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATC
* *
1488212 TTAGCTCCCTAAGCAGTAGGGA
66 TTAACCCCCTAAGCAGTAGGGA
*
1488234 AACAGATCGAAGACGAAGGGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAATTTACAGATC
1 AACAGATCGAAGACGAAGGGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATC
*
1488299 TTAACGCCCTAAGCAGTAGGGA
66 TTAACCCCCTAAGCAGTAGGGA
* *
1488321 AACAGATCAAAGACGAAGGGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAAATC
1 AACAGATCGAAGACGAAGGGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATC
1488386 TTAACCCCCTAAG
66 TTAACCCCCTAAG
1488399 TAGCAAGGTA
Statistics
Matches: 238, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 238 1.00
ACGTcount: A:0.36, C:0.24, G:0.23, T:0.18
Consensus pattern (87 bp):
AACAGATCGAAGACGAAGGGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATC
TTAACCCCCTAAGCAGTAGGGA
Found at i:1488282 original size:44 final size:44
Alignment explanation
Indices: 1488058--1488369 Score: 250
Period size: 44 Copynumber: 7.2 Consensus size: 44
1488048 AAAGAATGGT
*
1488058 GTAACAGATCGAAGACGAAGGGCCTTAACCCCCTAAGCAGTAGA
1 GTAACAGATCGAAGACGAAGGGCCTTAACCCCCTAAGCAGTAGG
* * ** * *
1488102 GTAACAG-GCTGAATTTAC--A-GATCTTAGCCCCCTAAGCAGTAAG
1 GTAACAGATC-GAA--GACGAAGGGCCTTAACCCCCTAAGCAGTAGG
* *
1488145 GAAAGAGATCGAAGACGAAGGGCCTTAACCCCCTAAGCAGTAGG
1 GTAACAGATCGAAGACGAAGGGCCTTAACCCCCTAAGCAGTAGG
* * ** * *
1488189 GTAACA-AGCTGAATTTAC--A-GATCTTAGCTCCCTAAGCAGTAGG
1 GTAACAGATC-GAA--GACGAAGGGCCTTAACCCCCTAAGCAGTAGG
*
1488232 GAAACAGATCGAAGACGAAGGGCCTTAACCCCCTAAGCAGTAGG
1 GTAACAGATCGAAGACGAAGGGCCTTAACCCCCTAAGCAGTAGG
* * ** ** *
1488276 GTAACAG-GCTAA-ATTTACA-GATCTTAACGCCCTAAGCAGTAGG
1 GTAACAGATCGAAGA-CGA-AGGGCCTTAACCCCCTAAGCAGTAGG
* *
1488319 GAAACAGATCAAAGACGAAGGGCCTTAACCCCCTAAGCAGTAGG
1 GTAACAGATCGAAGACGAAGGGCCTTAACCCCCTAAGCAGTAGG
1488363 GTAACAG
1 GTAACAG
1488370 GCTGAATTTA
Statistics
Matches: 202, Mismatches: 47, Indels: 38
0.70 0.16 0.13
Matches are distributed among these distances:
41 4 0.02
42 1 0.00
43 92 0.46
44 100 0.50
45 1 0.00
46 4 0.02
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.17
Consensus pattern (44 bp):
GTAACAGATCGAAGACGAAGGGCCTTAACCCCCTAAGCAGTAGG
Found at i:1489173 original size:7 final size:7
Alignment explanation
Indices: 1489161--1489198 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
1489151 ACTAAAAGGT
1489161 GTTCTTG
1 GTTCTTG
1489168 GTTCTTG
1 GTTCTTG
1489175 GTTCTTG
1 GTTCTTG
1489182 GTTCTTG
1 GTTCTTG
1489189 GTTCTTG
1 GTTCTTG
1489196 GTT
1 GTT
1489199 ATTTTTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.00, C:0.13, G:0.29, T:0.58
Consensus pattern (7 bp):
GTTCTTG
Found at i:1490236 original size:3 final size:3
Alignment explanation
Indices: 1490230--1490306 Score: 50
Period size: 3 Copynumber: 25.7 Consensus size: 3
1490220 CATCATCATC
* * * * *
1490230 ATT ATT ATT GA-T ATT ATT ATT ATT ATT GTT ACTT TTT GTC ACT ATT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT
* * *
1490276 GTC ATT ATT A-T ATT ATT ACT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1490307 ACTTATATTC
Statistics
Matches: 55, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
2 3 0.05
3 49 0.89
4 3 0.05
ACGTcount: A:0.29, C:0.06, G:0.05, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:1494844 original size:19 final size:20
Alignment explanation
Indices: 1494816--1494854 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1494806 TAAGTTTTCT
*
1494816 AAAATTTTAAATAT-ATTAA
1 AAAATGTTAAATATAATTAA
*
1494835 AAAATGTTAAGTATAATTAA
1 AAAATGTTAAATATAATTAA
1494855 TTTTAAAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
AAAATGTTAAATATAATTAA
Found at i:1494878 original size:17 final size:17
Alignment explanation
Indices: 1494856--1494894 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1494846 TATAATTAAT
* *
1494856 TTTAAAAGTTTAGTATA
1 TTTAAAACTTTAATATA
1494873 TTTAAAACTTTAATATA
1 TTTAAAACTTTAATATA
*
1494890 CTTAA
1 TTTAA
1494895 TATATATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (17 bp):
TTTAAAACTTTAATATA
Found at i:1494966 original size:18 final size:18
Alignment explanation
Indices: 1494945--1495024 Score: 62
Period size: 18 Copynumber: 4.6 Consensus size: 18
1494935 TAAAAACTTC
1494945 AAAAAATTAAATATATTA
1 AAAAAATTAAATATATTA
1494963 AAAAAATT---TATATTA
1 AAAAAATTAAATATATTA
***
1494978 AATATTTTTAAA-A-ACTTA
1 AA-AAAATTAAATATA-TTA
*
1494996 AAAAATTTAAATATATTA
1 AAAAAATTAAATATATTA
1495014 AAAAATATTAA
1 AAAAA-ATTAA
1495025 GTACAACCAA
Statistics
Matches: 48, Mismatches: 6, Indels: 15
0.70 0.09 0.22
Matches are distributed among these distances:
15 9 0.19
16 3 0.06
17 8 0.17
18 23 0.48
19 5 0.10
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAAAATTAAATATATTA
Found at i:1495077 original size:71 final size:71
Alignment explanation
Indices: 1494993--1495136 Score: 225
Period size: 71 Copynumber: 2.0 Consensus size: 71
1494983 TTTTAAAAAC
* *
1494993 TTAAAAAATTTAAATATATTAAAAAATATTAAGTACAACCAATTTTAAAATGTTAATATATTTAG
1 TTAAAAAATTTAAATATATTAAAAAATATTAAGTACAACCAATTTTAAAATGTTAATATATTCAA
1495058 TATATT
66 TATATT
* * * * *
1495064 TTAAAAATTTTAAATATATTAAAAAATGTTAAGTATAACTAATTTTAAAATTTTAATATATTCAA
1 TTAAAAAATTTAAATATATTAAAAAATATTAAGTACAACCAATTTTAAAATGTTAATATATTCAA
1495129 TATATT
66 TATATT
1495135 TT
1 TT
1495137 TTAAAAATAT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 66 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.44
Consensus pattern (71 bp):
TTAAAAAATTTAAATATATTAAAAAATATTAAGTACAACCAATTTTAAAATGTTAATATATTCAA
TATATT
Found at i:1495254 original size:17 final size:18
Alignment explanation
Indices: 1495202--1495264 Score: 69
Period size: 17 Copynumber: 3.6 Consensus size: 18
1495192 GAAAAAAGAT
1495202 ATTTT-AATATATTTAAA
1 ATTTTAAATATATTTAAA
* *
1495219 A-TTTAAAAAAACTTTAAA
1 ATTTTAAATATA-TTTAAA
1495237 ATTTTAAATATA-TTAAA
1 ATTTTAAATATATTTAAA
*
1495254 AGTTTAAATAT
1 ATTTTAAATAT
1495265 GTTAAAAGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
16 3 0.08
17 20 0.53
18 7 0.18
19 8 0.21
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
ATTTTAAATATATTTAAA
Found at i:1495269 original size:17 final size:17
Alignment explanation
Indices: 1495232--1495272 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
1495222 TAAAAAAACT
*
1495232 TTAAAATTTTAAATATA
1 TTAAAAGTTTAAATATA
*
1495249 TTAAAAGTTTAAATATG
1 TTAAAAGTTTAAATATA
1495266 TTAAAAG
1 TTAAAAG
1495273 AAAATATTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (17 bp):
TTAAAAGTTTAAATATA
Found at i:1495932 original size:19 final size:20
Alignment explanation
Indices: 1495892--1495934 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1495882 AACAACCTTT
*
1495892 TAATTTTAGTCTTTAATATA
1 TAATTTTAGTCTTAAATATA
1495912 TAATTTTATGT-TTAAATTATA
1 TAATTTTA-GTCTTAAA-TATA
1495933 TA
1 TA
1495935 GATAATTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (20 bp):
TAATTTTAGTCTTAAATATA
Found at i:1497531 original size:30 final size:30
Alignment explanation
Indices: 1497497--1497597 Score: 100
Period size: 30 Copynumber: 3.4 Consensus size: 30
1497487 GTCGCAGAGT
*
1497497 AGTTCATATCACTCAGACATTGGCAGTTCA
1 AGTTCATATCACTCAGACATTGGCAGTTCG
* *
1497527 AGTTCACATCAC-CTGACA-TGGACAGTTCG
1 AGTTCATATCACTCAGACATTGG-CAGTTCG
* * *
1497556 AGTTCATATCA-TCCGCACATAGGCGGTTCG
1 AGTTCATATCACTCAG-ACATTGGCAGTTCG
*
1497586 AGTTCATTTCAC
1 AGTTCATATCAC
1497598 CCAAAGCAAC
Statistics
Matches: 58, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
28 3 0.05
29 23 0.40
30 30 0.52
31 2 0.03
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.29
Consensus pattern (30 bp):
AGTTCATATCACTCAGACATTGGCAGTTCG
Found at i:1497545 original size:29 final size:30
Alignment explanation
Indices: 1497497--1497566 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
1497487 GTCGCAGAGT
1497497 AGTTCATATCACTCAGACATTGG-CAGTTCA
1 AGTTCATATCACTCAGACA-TGGACAGTTCA
* * *
1497527 AGTTCACATCAC-CTGACATGGACAGTTCG
1 AGTTCATATCACTCAGACATGGACAGTTCA
1497556 AGTTCATATCA
1 AGTTCATATCA
1497567 TCCGCACATA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 3 0.09
29 21 0.60
30 11 0.31
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (30 bp):
AGTTCATATCACTCAGACATGGACAGTTCA
Found at i:1500905 original size:12 final size:13
Alignment explanation
Indices: 1500855--1500905 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 13
1500845 ATTTGAATAT
1500855 TTTTAAAATTA-A
1 TTTTAAAATTATA
1500867 TTTTAAAATTAATAA
1 TTTTAAAATT-AT-A
1500882 TTTATAAAAATTATA
1 TTT-T-AAAATTATA
1500897 -TTTAAAATT
1 TTTTAAAATT
1500906 TAAAAATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
12 16 0.47
13 2 0.06
14 2 0.06
15 5 0.15
16 3 0.09
17 6 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TTTTAAAATTATA
Found at i:1500920 original size:29 final size:28
Alignment explanation
Indices: 1500856--1500945 Score: 76
Period size: 29 Copynumber: 3.0 Consensus size: 28
1500846 TTTGAATATT
*
1500856 TTTAAAATTAATTTTAAAA-TTAATAAT-
1 TTTAAAATTAA-TTTAAAATTTAAAAATA
1500883 TTATAAAAATTATATTTAAAATTTAAAAATA
1 TT-T-AAAATTA-ATTTAAAATTTAAAAATA
*
1500914 TTTAAAATATACATTAAAAATATTATAAAATA
1 TTTAAAAT-TA-ATTTAAAAT-TTA-AAAATA
1500946 AATAATAAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
27 2 0.04
28 1 0.02
29 19 0.37
30 19 0.37
31 5 0.10
32 6 0.12
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (28 bp):
TTTAAAATTAATTTAAAATTTAAAAATA
Found at i:1500954 original size:23 final size:22
Alignment explanation
Indices: 1500906--1500954 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
1500896 ATTTAAAATT
* *
1500906 TAAAAATATTTAAAATATACAT
1 TAAAAATATTTAAAATAAACAA
*
1500928 TAAAAATATTATAAAATAAATAA
1 TAAAAATATT-TAAAATAAACAA
1500951 TAAA
1 TAAA
1500955 TTTGAAAGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAAATATTTAAAATAAACAA
Found at i:1501011 original size:10 final size:9
Alignment explanation
Indices: 1500987--1501049 Score: 58
Period size: 10 Copynumber: 6.8 Consensus size: 9
1500977 AATAATATAT
1500987 TTTAAAAAA
1 TTTAAAAAA
1500996 -TTAAAAATA
1 TTTAAAAA-A
1501005 TTTAAAAAA
1 TTTAAAAAA
1501014 TTATAAAACAA
1 TT-TAAAA-AA
*
1501025 ATTAAAAAA
1 TTTAAAAAA
*
1501034 TATT-TAAAA
1 T-TTAAAAAA
1501043 TTTAAAA
1 TTTAAAA
1501050 TATACATTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
8 9 0.20
9 13 0.30
10 19 0.43
11 3 0.07
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:1501153 original size:21 final size:20
Alignment explanation
Indices: 1501120--1501159 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
1501110 TAAATGTTTT
1501120 ATATTATTAAAAATATATTTA
1 ATATTATTAAAAATA-ATTTA
1501141 ATATT-TTAAAAAATAATTT
1 ATATTATT-AAAAATAATTT
1501160 CAAATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATATTATTAAAAATAATTTA
Found at i:1501195 original size:23 final size:22
Alignment explanation
Indices: 1501165--1501229 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 22
1501155 AATTTCAAAT
1501165 ATATATATTTAAAATTTTTAAAA
1 ATATATATTTAAAATTTTT-AAA
* * *
1501188 ATATATATTATAAAGTATTTCAA
1 ATATATATT-TAAAATTTTTAAA
* *
1501211 ATATACATTTCAAATTTTT
1 ATATATATTTAAAATTTTT
1501230 TTAAAATGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
22 7 0.21
23 19 0.56
24 8 0.24
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.48
Consensus pattern (22 bp):
ATATATATTTAAAATTTTTAAA
Found at i:1504580 original size:26 final size:26
Alignment explanation
Indices: 1504546--1504598 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1504536 GTGAAGTAAA
1504546 AAAAAAAACCAATGTTTTTCTCCATT
1 AAAAAAAACCAATGTTTTTCTCCATT
1504572 AAAAAAAACCAATGTTTTTCTCCATT
1 AAAAAAAACCAATGTTTTTCTCCATT
1504598 A
1 A
1504599 CTGGCTTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.19, G:0.04, T:0.34
Consensus pattern (26 bp):
AAAAAAAACCAATGTTTTTCTCCATT
Found at i:1504843 original size:27 final size:29
Alignment explanation
Indices: 1504791--1504849 Score: 95
Period size: 27 Copynumber: 2.1 Consensus size: 29
1504781 TTTAATTAAT
*
1504791 TTTTTAAAATATTTAAAATATTTTTTATA
1 TTTTTAAAATATTAAAAATATTTTTTATA
1504820 TTTTT-AAAT-TTAAAAATATTTTTTATA
1 TTTTTAAAATATTAAAAATATTTTTTATA
1504847 TTT
1 TTT
1504850 CTTTTAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 20 0.69
28 4 0.14
29 5 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (29 bp):
TTTTTAAAATATTAAAAATATTTTTTATA
Found at i:1506802 original size:3 final size:3
Alignment explanation
Indices: 1506789--1506847 Score: 57
Period size: 3 Copynumber: 20.0 Consensus size: 3
1506779 ATAAGTAAAG
* * * * *
1506789 ATA AAA ATA ATA ATA ATA ATA ATA ATA ATG ATA GTA ATG ATA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
1506837 AGA AT- ATA ATA
1 ATA ATA ATA ATA
1506848 TATAGTATTA
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:1507117 original size:18 final size:18
Alignment explanation
Indices: 1507077--1507119 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
1507067 CACGTAATAT
* *
1507077 ATAAAAAATGTATCCGCA
1 ATAAAAAATATATACGCA
* *
1507095 TTAAAAAATATATACGTA
1 ATAAAAAATATATACGCA
1507113 ATAAAAA
1 ATAAAAA
1507120 TGCAATATTT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.58, C:0.09, G:0.07, T:0.26
Consensus pattern (18 bp):
ATAAAAAATATATACGCA
Found at i:1520714 original size:27 final size:28
Alignment explanation
Indices: 1520667--1520720 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
1520657 ATGAAATTTT
*
1520667 AAAAAAATAAAATATTATAAAAGTCATG
1 AAAAAAATAAAAAATTATAAAAGTCATG
* *
1520695 AAAAATATAAAAAATT-TAAAATTCAT
1 AAAAAAATAAAAAATTATAAAAGTCAT
1520721 TATCAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.28
Consensus pattern (28 bp):
AAAAAAATAAAAAATTATAAAAGTCATG
Found at i:1520811 original size:20 final size:20
Alignment explanation
Indices: 1520788--1520829 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1520778 ATTTTTAACT
1520788 AAATATTAAAAT-AAAAATAA
1 AAAT-TTAAAATCAAAAATAA
* *
1520808 AAATTTAGAATCAAAACTAA
1 AAATTTAAAATCAAAAATAA
1520828 AA
1 AA
1520830 TAAATAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (20 bp):
AAATTTAAAATCAAAAATAA
Found at i:1520856 original size:17 final size:18
Alignment explanation
Indices: 1520820--1520857 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1520810 ATTTAGAATC
1520820 AAAACTAAAATAAATAAT
1 AAAACTAAAATAAATAAT
* *
1520838 AAAATTAAATTAAAT-AT
1 AAAACTAAAATAAATAAT
1520855 AAA
1 AAA
1520858 GATATCAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAACTAAAATAAATAAT
Found at i:1522317 original size:17 final size:17
Alignment explanation
Indices: 1522292--1522324 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1522282 TTATTTTTTC
*
1522292 TTTCTGAAAACCCATTG
1 TTTCAGAAAACCCATTG
1522309 TTTCAGAAAACCCATT
1 TTTCAGAAAACCCATT
1522325 TCTTCTTCCA
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:0.33, C:0.24, G:0.09, T:0.33
Consensus pattern (17 bp):
TTTCAGAAAACCCATTG
Found at i:1523587 original size:15 final size:15
Alignment explanation
Indices: 1523557--1523617 Score: 54
Period size: 14 Copynumber: 4.1 Consensus size: 15
1523547 GACTAAAATA
*
1523557 TTAATTTTTAAGTTTT
1 TTAATTTTTTA-TTTT
1523573 TTAATTTTTTA-TTT
1 TTAATTTTTTATTTT
* **
1523587 TTAA-ATTTTAAATT
1 TTAATTTTTTATTTT
*
1523601 TTAAATTTTTATTTT
1 TTAATTTTTTATTTT
1523616 TT
1 TT
1523618 GAGTTTATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
13 5 0.14
14 13 0.35
15 9 0.24
16 10 0.27
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (15 bp):
TTAATTTTTTATTTT
Found at i:1523589 original size:14 final size:14
Alignment explanation
Indices: 1523570--1523616 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
1523560 ATTTTTAAGT
*
1523570 TTTTTAATTTTTTA
1 TTTTTAAATTTTTA
*
1523584 TTTTTAAATTTTAA
1 TTTTTAAATTTTTA
*
1523598 ATTTTAAATTTTTA
1 TTTTTAAATTTTTA
1523612 TTTTT
1 TTTTT
1523617 TGAGTTTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTTAAATTTTTA
Found at i:1523610 original size:8 final size:8
Alignment explanation
Indices: 1523559--1523611 Score: 58
Period size: 7 Copynumber: 7.0 Consensus size: 8
1523549 CTAAAATATT
1523559 AATTTTTA
1 AATTTTTA
* *
1523567 AGTTTTTT
1 AATTTTTA
1523575 AATTTTT-
1 AATTTTTA
*
1523582 TATTTTTA
1 AATTTTTA
1523590 AA-TTTTA
1 AATTTTTA
1523597 AA-TTTTA
1 AATTTTTA
1523604 AATTTTTA
1 AATTTTTA
1523612 TTTTTTGAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
7 20 0.53
8 18 0.47
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (8 bp):
AATTTTTA
Found at i:1523630 original size:28 final size:28
Alignment explanation
Indices: 1523569--1523631 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
1523559 AATTTTTAAG
* *
1523569 TTTTTTAATTTTTTATTTTTAAATTTTA
1 TTTTTTAAATTTTTATTTTTAAAGTTTA
** **
1523597 AATTTTAAATTTTTATTTTTTGAGTTTA
1 TTTTTTAAATTTTTATTTTTAAAGTTTA
1523625 TTTTTTA
1 TTTTTTA
1523632 TTTCGATTTA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.71
Consensus pattern (28 bp):
TTTTTTAAATTTTTATTTTTAAAGTTTA
Found at i:1524227 original size:7 final size:7
Alignment explanation
Indices: 1524215--1524278 Score: 56
Period size: 7 Copynumber: 9.0 Consensus size: 7
1524205 CCCATGGCCA
1524215 TTAAACC
1 TTAAACC
1524222 TTAAACC
1 TTAAACC
*
1524229 ATAAAACC
1 -TTAAACC
*
1524237 CTAAACC
1 TTAAACC
* *
1524244 ATAGACC
1 TTAAACC
1524251 TTAAACC
1 TTAAACC
**
1524258 TTAAATA
1 TTAAACC
1524265 TTAAACC
1 TTAAACC
*
1524272 GTAAACC
1 TTAAACC
1524279 AAAAAATAAA
Statistics
Matches: 44, Mismatches: 12, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
7 38 0.86
8 6 0.14
ACGTcount: A:0.47, C:0.27, G:0.03, T:0.23
Consensus pattern (7 bp):
TTAAACC
Found at i:1524235 original size:15 final size:15
Alignment explanation
Indices: 1524212--1524262 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
1524202 ATACCCATGG
*
1524212 CCATTAAACCTTAAA
1 CCATAAAACCTTAAA
*
1524227 CCATAAAACCCTAAA
1 CCATAAAACCTTAAA
*
1524242 CCAT-AGACCTTAAA
1 CCATAAAACCTTAAA
*
1524256 CCTTAAA
1 CCATAAA
1524263 TATTAAACCG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
14 11 0.38
15 18 0.62
ACGTcount: A:0.47, C:0.29, G:0.02, T:0.22
Consensus pattern (15 bp):
CCATAAAACCTTAAA
Found at i:1524559 original size:41 final size:41
Alignment explanation
Indices: 1524500--1524746 Score: 316
Period size: 41 Copynumber: 6.0 Consensus size: 41
1524490 AGGAGTTATA
* *
1524500 TGACTTTTAGCGGCGTTTTATCAAAAGCGCCGCTAATGCTC
1 TGACTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTC
* * *
1524541 TGACTTTTAGCGGTGTTTTACCGAAAGCGCCGCTGTTGCTC
1 TGACTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTC
* * * *
1524582 CGACTTTTAGCGGCGTTTTACCGAAAGCACCGCTATTGGTC
1 TGACTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTC
** * *
1524623 TGACTTTTAGCGGCGTTTTACCGGAAGCGTCGCTATTACTC
1 TGACTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTC
**
1524664 TGACTTTTAGCGGCGTTTTACCAAAAGCGTTGCTATTGCTC
1 TGACTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTC
* * * *
1524705 TG-TTTTTAGTGGCGTTTTACCAAAAACGCCGCTATTGATC
1 TGACTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTC
1524745 TG
1 TG
1524747 TATTTTACAA
Statistics
Matches: 180, Mismatches: 26, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 0.19
41 146 0.81
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.34
Consensus pattern (41 bp):
TGACTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTC
Done.