Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 15 of 292
Found at i:4164449 original size:12 final size:12
Alignment explanation
Indices: 4164432--4164464 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
4164422 CATTAATATC
4164432 TATATATATCAA
1 TATATATATCAA
*
4164444 TATATATATCCA
1 TATATATATCAA
4164456 TATATATAT
1 TATATATAT
4164465 TATTTATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (12 bp):
TATATATATCAA
Found at i:4168261 original size:43 final size:43
Alignment explanation
Indices: 4168214--4168345 Score: 203
Period size: 43 Copynumber: 3.1 Consensus size: 43
4168204 AAAAATGCCG
* *
4168214 CTAAAGGTCATGTTCTTTAGCGGCGTTTGTGTGTAAAGCACCA
1 CTAAAGGTCATGTTCTATAGCGGCGTTTGTGTGTAAAACACCA
* *
4168257 CTAAAGGTCATGTTCTATAGCGGCATTTGTGTGTAAAACGCCA
1 CTAAAGGTCATGTTCTATAGCGGCGTTTGTGTGTAAAACACCA
* *
4168300 CTAAAGGTCATGTTCTATAGCGGCGTTTGTG-GGAAATCACCA
1 CTAAAGGTCATGTTCTATAGCGGCGTTTGTGTGTAAAACACCA
4168342 CTAA
1 CTAA
4168346 CTTTAACAGA
Statistics
Matches: 81, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
42 12 0.15
43 69 0.85
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (43 bp):
CTAAAGGTCATGTTCTATAGCGGCGTTTGTGTGTAAAACACCA
Found at i:4170279 original size:6 final size:5
Alignment explanation
Indices: 4170258--4170292 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
4170248 TGAAAATGTG
4170258 AAAAT AAAAT AAAAT AAAAAT AAAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT -AAAAT -AAAAT AAAAT AAA
4170293 GAACACACAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 18 0.62
6 11 0.38
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:4170279 original size:11 final size:11
Alignment explanation
Indices: 4170258--4170292 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
4170248 TGAAAATGTG
4170258 AAAATAAAAT-
1 AAAATAAAATA
4170268 AAAATAAAAATA
1 AAAAT-AAAATA
4170280 AAAATAAAATA
1 AAAATAAAATA
4170291 AA
1 AA
4170293 GAACACACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.22
11 13 0.57
12 5 0.22
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:4174721 original size:11 final size:11
Alignment explanation
Indices: 4174700--4174728 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4174690 CCAATTTGTG
4174700 AAAAT-AAAAT
1 AAAATAAAAAT
4174710 AAAATAAAAAT
1 AAAATAAAAAT
4174721 AAAATAAA
1 AAAATAAA
4174729 GAACACACAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:4175773 original size:9 final size:10
Alignment explanation
Indices: 4175747--4175772 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
4175737 TCATATTTTT
4175747 TAAAAAATTC
1 TAAAAAATTC
4175757 TAAAAAATTC
1 TAAAAAATTC
4175767 TAAAAA
1 TAAAAA
4175773 TATATAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (10 bp):
TAAAAAATTC
Found at i:4188107 original size:259 final size:257
Alignment explanation
Indices: 4187641--4188165 Score: 982
Period size: 259 Copynumber: 2.0 Consensus size: 257
4187631 TCATTTTACC
4187641 CACA-AGCTT-GTAAGAGTCCTATATTCACTATATTGTACCATTTCTTATTTTTTCCTCTCAAAT
1 CACACAGCTTCGTAAGAGTCCTATATTCACTATATTGTACCATTTCTTATTTTTTCCTCTCAAAT
4187704 ATTTTGAAATCACCAAGATACCTCTACCTAAACTCGAGTTATCTATGGCCTGATAGTTTCAATAT
66 ATTTTGAAATCACCAAGATACCTCTACCTAAACTCGAGTTATCTATGGCCTGATAGTTTCAATAT
** *
4187769 TACTGATCATTAAGAAGTGTCATAAGGATCAATTATGGGAACTAGGGATAAATAGCATATTGGTA
131 TACCAATCATTAAGAAGTGTCATAAGGATCAATTATGGGAACTAGGGATAAATAGCATATTGGCA
4187834 TGGTTATCTGAGAATTAGTTATTCAAACAATGCTTTAGGTCATCCCTAAGCATTCCACCATA
196 TGGTTATCTGAGAATTAGTTATTCAAACAATGCTTTAGGTCATCCCTAAGCATTCCACCATA
4187896 CACACAGCTTCGTAAGAGTCCTATATTCACTATATTGTACCATTTCTTATTTTTTCCTCTCAAAT
1 CACACAGCTTCGTAAGAGTCCTATATTCACTATATTGTACCATTTCTTATTTTTTCCTCTCAAAT
4187961 ATTTTGAAATCACCAAGATACCTCTACCTAAACACTCGAGTTATCTATGGCCTGATAGTTTCAAT
66 ATTTTGAAATCACCAAGATACCTCTACCT-AA-ACTCGAGTTATCTATGGCCTGATAGTTTCAAT
4188026 ATTACCAATCATTAAGAAGTGTCATAAGGATCAATTATGGGAACTAGGGATAAATAGCATATTGG
129 ATTACCAATCATTAAGAAGTGTCATAAGGATCAATTATGGGAACTAGGGATAAATAGCATATTGG
*
4188091 CATGGTTATTTGAGAATTAGTTATTCAAACAATGCTTTAGGTCATCCCTAAGCATTCCACCATA
194 CATGGTTATCTGAGAATTAGTTATTCAAACAATGCTTTAGGTCATCCCTAAGCATTCCACCATA
4188155 CACACAGCTTC
1 CACACAGCTTC
4188166 TTTCATACTT
Statistics
Matches: 262, Mismatches: 4, Indels: 4
0.97 0.01 0.01
Matches are distributed among these distances:
255 4 0.02
256 5 0.02
257 83 0.32
258 2 0.01
259 168 0.64
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (257 bp):
CACACAGCTTCGTAAGAGTCCTATATTCACTATATTGTACCATTTCTTATTTTTTCCTCTCAAAT
ATTTTGAAATCACCAAGATACCTCTACCTAAACTCGAGTTATCTATGGCCTGATAGTTTCAATAT
TACCAATCATTAAGAAGTGTCATAAGGATCAATTATGGGAACTAGGGATAAATAGCATATTGGCA
TGGTTATCTGAGAATTAGTTATTCAAACAATGCTTTAGGTCATCCCTAAGCATTCCACCATA
Found at i:4193358 original size:39 final size:39
Alignment explanation
Indices: 4193227--4193390 Score: 215
Period size: 40 Copynumber: 4.2 Consensus size: 39
4193217 GGACTAAGAT
* **
4193227 CCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTA-AAC
* * *
4193267 CCGAAGGCATTTATGCTAG-TGATTATATCCGGGCTAAGAC
1 CCGAAGGCATTTGTGCGAGTTG-CTATATCCGGGCTAA-AC
4193307 CCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAAC
1 CCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAAC
*
4193346 CCGAAGGCATTTGTGCGAGTTGTTATATCC-GGCTAAATC
1 CCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAA-C
4193385 CCGAAG
1 CCGAAG
4193391 ATACTTGGGT
Statistics
Matches: 110, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
38 7 0.06
39 40 0.36
40 61 0.55
41 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (39 bp):
CCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAAC
Found at i:4193658 original size:22 final size:22
Alignment explanation
Indices: 4193618--4193659 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
4193608 GAATGTGCAT
*
4193618 ATATGAAGTTATTCATTTAGCC
1 ATATGAAGTTATACATTTAGCC
4193640 ATATGAATGTTATAC-TTTAG
1 ATATGAA-GTTATACATTTAG
4193660 TCAAAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (22 bp):
ATATGAAGTTATACATTTAGCC
Found at i:4201319 original size:40 final size:40
Alignment explanation
Indices: 4201240--4201416 Score: 225
Period size: 40 Copynumber: 4.5 Consensus size: 40
4201230 CGGATGATAA
* * * *
4201240 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * * *
4201280 CCGGGCTATGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
*
4201320 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
*
4201360 CCAGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
4201400 CC-GGCTAA-ATCCCGAAG
1 CCGGGCTAAGA-CCCGAAG
4201417 ATACTTGGGT
Statistics
Matches: 119, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.01
39 15 0.13
40 101 0.85
41 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:4201684 original size:22 final size:22
Alignment explanation
Indices: 4201644--4201685 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
4201634 GAATGTGCAT
*
4201644 ATATGAAGTTATTCATTTAGCC
1 ATATGAAGTTATACATTTAGCC
4201666 ATATGAATGTTATAC-TTTAG
1 ATATGAA-GTTATACATTTAG
4201686 TCAAAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (22 bp):
ATATGAAGTTATACATTTAGCC
Found at i:4215671 original size:33 final size:34
Alignment explanation
Indices: 4215623--4215689 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
4215613 ATATTTTATA
*
4215623 ATTTTTTAAATTTTTTAAT-AATTATTAATAATTT
1 ATTTTTTAAATTTTTTAATAAAAT-TTAATAATTT
*
4215657 ATTTTTTATATTTTTT-ATAAAATTTAATAATTT
1 ATTTTTTAAATTTTTTAATAAAATTTAATAATTT
4215690 TTACATTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 12 0.40
34 18 0.60
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (34 bp):
ATTTTTTAAATTTTTTAATAAAATTTAATAATTT
Found at i:4216800 original size:31 final size:31
Alignment explanation
Indices: 4216765--4216823 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
4216755 GTGTAATTCA
4216765 TATTCGAGTTAAACCAAAAAACTTAATTTTT
1 TATTCGAGTTAAACCAAAAAACTTAATTTTT
* * * *
4216796 TATTCGAGTTGATCCGAATAACTTAATT
1 TATTCGAGTTAAACCAAAAAACTTAATT
4216824 AACTCAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (31 bp):
TATTCGAGTTAAACCAAAAAACTTAATTTTT
Found at i:4217803 original size:32 final size:32
Alignment explanation
Indices: 4217767--4217831 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
4217757 CAATAAGTTA
4217767 TAGTGGTGTTAGGTGACAGTTTAGGTAAAATT
1 TAGTGGTGTTAGGTGACAGTTTAGGTAAAATT
4217799 TAGTGGTGTTAGGTGACAGTTTAGGTAAAATT
1 TAGTGGTGTTAGGTGACAGTTTAGGTAAAATT
4217831 T
1 T
4217832 GCTTCTAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.28, C:0.03, G:0.31, T:0.38
Consensus pattern (32 bp):
TAGTGGTGTTAGGTGACAGTTTAGGTAAAATT
Found at i:4230496 original size:26 final size:26
Alignment explanation
Indices: 4230465--4230572 Score: 173
Period size: 26 Copynumber: 4.2 Consensus size: 26
4230455 TGAAATGCCC
4230465 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
*
4230491 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
* *
4230517 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAAACCATT
4230543 ATCATGGAACATTTACCT-AACCTATT
1 ATCATGGAACATTTACCTAAACC-ATT
4230569 ATCA
1 ATCA
4230573 ATTTGTACCA
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
25 3 0.04
26 73 0.96
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:4236010 original size:25 final size:27
Alignment explanation
Indices: 4235973--4236025 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
4235963 TCAAACATGC
4235973 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
4235999 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
4236025 A
1 A
4236026 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:4237530 original size:26 final size:26
Alignment explanation
Indices: 4237499--4237606 Score: 173
Period size: 26 Copynumber: 4.2 Consensus size: 26
4237489 TGAAATGCCC
4237499 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
*
4237525 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
* *
4237551 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAAACCATT
4237577 ATCATGGAACATTTACCT-AACCTATT
1 ATCATGGAACATTTACCTAAACC-ATT
4237603 ATCA
1 ATCA
4237607 ATTTGTACCA
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
25 3 0.04
26 73 0.96
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:4240616 original size:92 final size:91
Alignment explanation
Indices: 4240413--4240608 Score: 295
Period size: 91 Copynumber: 2.2 Consensus size: 91
4240403 ACTCTTTGTA
* * *
4240413 TAAGGGTTGGGAGATGCATGTCTAAAGCAACGCTTAAATAAGAGTTGCCTTTGTGTAGTCCTAAG
1 TAAGGGTTGGGATATGTATGCCTAAAGCAACGCTTAAATAAGAGTTGCCTTTGTGTAGTCCTAAG
*
4240478 ACGACACTTTTGTGGCGACATTTTCC
66 ACGACACTTTTGTGACGACATTTTCC
* * **
4240504 TAAGGGTTGGTATATGTATGCCTAAAGCAACGCTTGAATAAGAGTTGGTTTTTGTGTAGTCCTAA
1 TAAGGGTTGGGATATGTATGCCTAAAGCAACGCTTAAATAAGAGTT-GCCTTTGTGTAGTCCTAA
4240569 GACGACACTTTTGTGACGACA-TTTCC
65 GACGACACTTTTGTGACGACATTTTCC
*
4240595 TAAGTGTTGGGATA
1 TAAGGGTTGGGATA
4240609 GACTATGCTT
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
91 58 0.62
92 36 0.38
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.33
Consensus pattern (91 bp):
TAAGGGTTGGGATATGTATGCCTAAAGCAACGCTTAAATAAGAGTTGCCTTTGTGTAGTCCTAAG
ACGACACTTTTGTGACGACATTTTCC
Found at i:4240784 original size:132 final size:132
Alignment explanation
Indices: 4240504--4241004 Score: 788
Period size: 132 Copynumber: 3.8 Consensus size: 132
4240494 GACATTTTCC
* * * *
4240504 TAAGGGTTGGTATATGTATGCCTAAAGCAACGCTTGAATAAGAGTTGGTTTTTGTGTAGTCCTAA
1 TAAGGGTTGGGATATGTATGCCTAAGGCAACGCTTGAATAAGAGTTGGCTTTTGTCTAGTCCTAA
*
4240569 GACGACACTTTTGTGACGACA-TTTCCTAAGTGTTGGGATAGACTATGCTTTGGCCAACTCTTTG
66 GACGACACTTTTGTGGCGACACTTTCCTAAGTGTTGGGATAGACTATGCTTTGGCCAACTCTTTG
4240633 TA
131 TA
* * * *
4240635 TAAGGGTTAGGATATGTATACCTAAGGCAACGCTTGAATAAGAGTTGGCTTCTGTGTAGTCCTAA
1 TAAGGGTTGGGATATGTATGCCTAAGGCAACGCTTGAATAAGAGTTGGCTTTTGTCTAGTCCTAA
** * *
4240700 GAAAACACTTTTGTGGTGACACTTCCCTAAGTGTTGGGATAGACTATGCTTTGGCCAACTCTTTG
66 GACGACACTTTTGTGGCGACACTTTCCTAAGTGTTGGGATAGACTATGCTTTGGCCAACTCTTTG
4240765 TA
131 TA
* *
4240767 TAAGGGTTGGGATATGTATGCCTAAGGCAACGCTTGAATAAGAATTGGCTTTTGTCTAATCCTAA
1 TAAGGGTTGGGATATGTATGCCTAAGGCAACGCTTGAATAAGAGTTGGCTTTTGTCTAGTCCTAA
* * * *
4240832 GATGACACTTTTGTAGCGACACTTTTCTAAGTGTTGGGATAGACTACGCTTTGGCCAACTCTTTG
66 GACGACACTTTTGTGGCGACACTTTCCTAAGTGTTGGGATAGACTATGCTTTGGCCAACTCTTTG
4240897 TA
131 TA
*
4240899 TAAGGGTTGGGATATGTATGCCTAAGACAACGCTTGAATAAGAGTTGGCTTTTGTCTAGTCCTAA
1 TAAGGGTTGGGATATGTATGCCTAAGGCAACGCTTGAATAAGAGTTGGCTTTTGTCTAGTCCTAA
* * *
4240964 GACGACAGTTTTGGGGTGACACTTTCCTAAGTGTTGGGATA
66 GACGACACTTTTGTGGCGACACTTTCCTAAGTGTTGGGATA
4241005 CACTTCTCAG
Statistics
Matches: 336, Mismatches: 33, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
131 76 0.23
132 260 0.77
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.34
Consensus pattern (132 bp):
TAAGGGTTGGGATATGTATGCCTAAGGCAACGCTTGAATAAGAGTTGGCTTTTGTCTAGTCCTAA
GACGACACTTTTGTGGCGACACTTTCCTAAGTGTTGGGATAGACTATGCTTTGGCCAACTCTTTG
TA
Found at i:4241295 original size:21 final size:21
Alignment explanation
Indices: 4241248--4241295 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
4241238 TTAGTTTAGG
* * *
4241248 GTTTAAGGTTTAGTGCTTAAA
1 GTTTATGGTTTAGGGATTAAA
* *
4241269 GATTATGGTTTAGGGATTATA
1 GTTTATGGTTTAGGGATTAAA
4241290 GTTTAT
1 GTTTAT
4241296 ATAGTTTAAG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.46
Consensus pattern (21 bp):
GTTTATGGTTTAGGGATTAAA
Found at i:4241331 original size:15 final size:15
Alignment explanation
Indices: 4241313--4241347 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
4241303 AAGGTTTTAA
*
4241313 GGTTTTGTGTTTATG
1 GGTTTTATGTTTATG
4241328 GGTTTTATGTTTATG
1 GGTTTTATGTTTATG
4241343 GGTTT
1 GGTTT
4241348 GGGGTTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.09, C:0.00, G:0.31, T:0.60
Consensus pattern (15 bp):
GGTTTTATGTTTATG
Found at i:4241340 original size:37 final size:39
Alignment explanation
Indices: 4241283--4241369 Score: 99
Period size: 37 Copynumber: 2.3 Consensus size: 39
4241273 ATGGTTTAGG
*
4241283 GATTATA-GTTTATATAGTTTAAGGTTTTAAGGTTTTGT
1 GATTATAGGTTTATATAGTTTAAGGGTTTAAGGTTTTGT
* * * **
4241321 GTTTATGGGTTT-TAT-GTTTATGGGTTTGGGGTTTTGT
1 GATTATAGGTTTATATAGTTTAAGGGTTTAAGGTTTTGT
4241358 GATTATAGGTTT
1 GATTATAGGTTT
4241370 GCGATTAATC
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
37 28 0.70
38 8 0.20
39 4 0.10
ACGTcount: A:0.18, C:0.00, G:0.28, T:0.54
Consensus pattern (39 bp):
GATTATAGGTTTATATAGTTTAAGGGTTTAAGGTTTTGT
Found at i:4241352 original size:22 final size:22
Alignment explanation
Indices: 4241327--4241370 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
4241317 TTGTGTTTAT
* *
4241327 GGGTTTTATGTTTATGGGTTTG
1 GGGTTTTATGATTATAGGTTTG
*
4241349 GGGTTTTGTGATTATAGGTTTG
1 GGGTTTTATGATTATAGGTTTG
4241371 CGATTAATCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.11, C:0.00, G:0.36, T:0.52
Consensus pattern (22 bp):
GGGTTTTATGATTATAGGTTTG
Found at i:4242082 original size:44 final size:45
Alignment explanation
Indices: 4241985--4242102 Score: 166
Period size: 44 Copynumber: 2.6 Consensus size: 45
4241975 TTAAGAATGT
4241985 ATGCATACTTTACCCAGATAAAGTATGTATTAGCAGATTCACTAATA
1 ATGCATACTTTACCCAGATAAAGTATG--TTAGCAGATTCACTAATA
* *
4242032 ATGCATACTTTACCCGGATAAAGTATG-TAGTAGATTCACTAATA
1 ATGCATACTTTACCCAGATAAAGTATGTTAGCAGATTCACTAATA
* * *
4242076 ATGCATACTTTATCTAGGTAAAGTATG
1 ATGCATACTTTACCCAGATAAAGTATG
4242103 CATTATTTAT
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
44 39 0.60
47 26 0.40
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (45 bp):
ATGCATACTTTACCCAGATAAAGTATGTTAGCAGATTCACTAATA
Found at i:4244809 original size:7 final size:6
Alignment explanation
Indices: 4244766--4244808 Score: 59
Period size: 6 Copynumber: 6.8 Consensus size: 6
4244756 TTCAATCTTT
*
4244766 ATTTTA ATTTTA ATTTTA ATTTTGT ATTTTAA ATTTTA ATTTT
1 ATTTTA ATTTTA ATTTTA ATTTT-A ATTTT-A ATTTTA ATTTT
4244809 TTTAGTTGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
6 23 0.70
7 10 0.30
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (6 bp):
ATTTTA
Found at i:4244969 original size:39 final size:37
Alignment explanation
Indices: 4244915--4245251 Score: 154
Period size: 37 Copynumber: 9.1 Consensus size: 37
4244905 ATTATACGTG
* * *
4244915 TCTATCCCAATCTTTTTTTATAGGTTGTTTTAAATAATA
1 TCTATCCCAACCTTTTTTTA-AGGTTGCTTTAAA-AAGA
* *
4244954 TCTATCCCAACC--TTTTTAAGGTTGCTTTAAACAGG
1 TCTATCCCAACCTTTTTTTAAGGTTGCTTTAAAAAGA
* * * * * * *
4244989 TCTATCCCAACCTTTTTTAAAAGTTACCTTAGACATGG
1 TCTATCCCAACCTTTTTTTAAGGTTGCTTTA-AAAAGA
* * *
4245027 TCTATCCCAACC--TTTTTAAGGTTGCCTT-AGACGA
1 TCTATCCCAACCTTTTTTTAAGGTTGCTTTAAAAAGA
* * * * * * *
4245061 GTCTATTCCGACCTTTTTTAAAGGTTGCCTTAGACATGG
1 -TCTATCCCAACCTTTTTTTAAGGTTGCTTTA-AAAAGA
* * * * * *
4245100 TCTATCCTAACC--TGTTTAAGGTTGCCTTAGATAGG
1 TCTATCCCAACCTTTTTTTAAGGTTGCTTTAAAAAGA
* *
4245135 TCTATCCCAACCTTTTTTTATAGGTTGTTTTAGACAATG-
1 TCTATCCCAACCTTTTTTTA-AGGTTGCTTTA-A-AAAGA
* * * ** *
4245174 TCGATCCCAACC--TTTTTAAGGTTGCATTAGACGGC
1 TCTATCCCAACCTTTTTTTAAGGTTGCTTTAAAAAGA
* * * *
4245209 TCTATCCCAACCGTTTTTAAAAGTTGCCTTAAACAAGA
1 TCTATCCCAACCTTTTTTTAAGGTTGCTTTAAA-AAGA
*
4245247 ACTAT
1 TCTAT
4245252 ATCGACCTTT
Statistics
Matches: 226, Mismatches: 55, Indels: 35
0.72 0.17 0.11
Matches are distributed among these distances:
34 5 0.02
35 47 0.21
36 49 0.22
37 60 0.27
38 38 0.17
39 25 0.11
40 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (37 bp):
TCTATCCCAACCTTTTTTTAAGGTTGCTTTAAAAAGA
Found at i:4245004 original size:74 final size:72
Alignment explanation
Indices: 4244914--4245239 Score: 350
Period size: 73 Copynumber: 4.4 Consensus size: 72
4244904 TATTATACGT
* * ** * *
4244914 GTCTATCCCAATCTTTTTTTATAGGTTGTTTTAAATAAT-ATCTATCCCAACCTTTTTAAGGTTG
1 GTCTATCCCAA-CCTTTTTTAAAGGTTGCCTTAGA-AATGGTCTATCCCAACCTTTTTAAGGTTG
* *
4244978 CTTTAAACAG
64 CCTTAGAC-G
* * *
4244988 GTCTATCCCAACCTTTTTTAAAAGTTACCTTAGACATGGTCTATCCCAACCTTTTTAAGGTTGCC
1 GTCTATCCCAACCTTTTTTAAAGGTTGCCTTAGAAATGGTCTATCCCAACCTTTTTAAGGTTGCC
4245053 TTAGACG
66 TTAGACG
* * * * *
4245060 AGTCTATTCCGACCTTTTTTAAAGGTTGCCTTAGACATGGTCTATCCTAACCTGTTTAAGGTTGC
1 -GTCTATCCCAACCTTTTTTAAAGGTTGCCTTAGAAATGGTCTATCCCAACCTTTTTAAGGTTGC
*
4245125 CTTAGATAG
65 CTTAGA-CG
* ** *
4245134 GTCTATCCCAACCTTTTTTTATAGGTTGTTTTAGACAAT-GTCGATCCCAACCTTTTTAAGGTTG
1 GTCTATCCCAACC-TTTTTTAAAGGTTGCCTTAGA-AATGGTCTATCCCAACCTTTTTAAGGTTG
*
4245198 CATTAGACG
64 CCTTAGACG
* *
4245207 GCTCTATCCCAACCGTTTTTAAAAGTTGCCTTA
1 G-TCTATCCCAACCTTTTTTAAAGGTTGCCTTA
4245240 AACAAGAACT
Statistics
Matches: 212, Mismatches: 34, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
72 3 0.01
73 137 0.65
74 70 0.33
75 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (72 bp):
GTCTATCCCAACCTTTTTTAAAGGTTGCCTTAGAAATGGTCTATCCCAACCTTTTTAAGGTTGCC
TTAGACG
Found at i:4245037 original size:73 final size:72
Alignment explanation
Indices: 4244954--4245338 Score: 373
Period size: 73 Copynumber: 5.3 Consensus size: 72
4244944 TTAAATAATA
* * *
4244954 TCTATCCCAACCTTTTTAAGGTTGCTTTAAACAGGTCTATCCCAACCTTTTTTAAAAGTTACCTT
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGAC-GGTCTATCCCAACCTTTTTTAAAAGTTGCCTT
4245019 AGACATGG
65 AGACATGG
* * *
4245027 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACGAGTCTATTCCGACCTTTTTTAAAGGTTGCCTT
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACG-GTCTATCCCAACCTTTTTTAAAAGTTGCCTT
4245092 AGACATGG
65 AGACATGG
* * * * * **
4245100 TCTATCCTAACCTGTTTAAGGTTGCCTTAGATAGGTCTATCCCAACCTTTTTTTATAGGTTGTTT
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGA-CGGTCTATCCCAACC-TTTTTTAAAAGTTGCCT
4245165 TAGACAAT-G
64 TAGAC-ATGG
* * *
4245174 TCGATCCCAACCTTTTTAAGGTTGCATTAGACGGCTCTATCCCAACCGTTTTTAAAAGTTGCCTT
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACGG-TCTATCCCAACCTTTTTTAAAAGTTGCCTT
* * *
4245239 AAACAAGA
65 AGACATGG
* ** * * * * * * * * *
4245247 ACTATATCGACC-TTTTAATGTTGTCTTAGACAGGTTTATCACAACCTTTTTCAAAGGTCGGTCT
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGAC-GGTCTATCCCAACCTTTTTTAAAAGT-TGCCT
4245311 TA-AC-TAGG
64 TAGACAT-GG
4245319 TCTATCCCAACCCTTTTTAA
1 TCTATCCCAA-CCTTTTTAA
4245339 AGGTCGGCTT
Statistics
Matches: 253, Mismatches: 48, Indels: 21
0.79 0.15 0.07
Matches are distributed among these distances:
72 46 0.18
73 139 0.55
74 66 0.26
75 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (72 bp):
TCTATCCCAACCTTTTTAAGGTTGCCTTAGACGGTCTATCCCAACCTTTTTTAAAAGTTGCCTTA
GACATGG
Found at i:4245204 original size:36 final size:35
Alignment explanation
Indices: 4244954--4245338 Score: 283
Period size: 37 Copynumber: 10.5 Consensus size: 35
4244944 TTAAATAATA
* * *
4244954 TCTATCCCAACCTTTTTAAGGTTGCTTTAAACAGG
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACATG
* *
4244989 TCTATCCCAACCTTTTTTAAAAGTTACCTTAGACATGG
1 TCTATCCCAACC-TTTTT-AAGGTTGCCTTAGACAT-G
4245027 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACGA-G
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGAC-ATG
* *
4245062 TCTATTCCGACCTTTTTTAAAGGTTGCCTTAGACATGG
1 TCTATCCCAACC-TTTTT-AAGGTTGCCTTAGACAT-G
* * * *
4245100 TCTATCCTAACCTGTTTAAGGTTGCCTTAGATAGG
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACATG
**
4245135 TCTATCCCAACCTTTTTTTATAGGTTGTTTTAGACAATG
1 TCTATCCCAACC--TTTTTA-AGGTTGCCTTAGAC-ATG
* * *
4245174 TCGATCCCAACCTTTTTAAGGTTGCATTAGAC-GG
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACATG
* * *
4245208 CTCTATCCCAACCGTTTTTAAAAGTTGCCTTAAACAAG
1 -TCTATCCCAACC-TTTTT-AAGGTTGCCTTAGACATG
* ** * * * *
4245246 AACTATATCGACC-TTTTAATGTTGTCTTAGACAGG
1 -TCTATCCCAACCTTTTTAAGGTTGCCTTAGACATG
* * * * *
4245281 TTTATCACAACCTTTTTCAAAGGTCGGTCTTA-ACTAGG
1 TCTATCCCAACCTTTTT--AAGGT-TGCCTTAGAC-ATG
4245319 TCTATCCCAACCCTTTTTAA
1 TCTATCCCAA-CCTTTTTAA
4245339 AGGTCGGCTT
Statistics
Matches: 280, Mismatches: 48, Indels: 42
0.76 0.13 0.11
Matches are distributed among these distances:
34 8 0.03
35 64 0.23
36 60 0.21
37 68 0.24
38 60 0.21
39 20 0.07
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (35 bp):
TCTATCCCAACCTTTTTAAGGTTGCCTTAGACATG
Found at i:4245226 original size:147 final size:146
Alignment explanation
Indices: 4244954--4245297 Score: 388
Period size: 147 Copynumber: 2.4 Consensus size: 146
4244944 TTAAATAATA
* *
4244954 TCTATCCCAACCTTTTTAAGGTTGCTTTAAACAGGTCTATCCCAACCTTTTTTAAAAGTTACCTT
1 TCTATCCCAACCTGTTTAAGGTTGCCTTAAACAGGTCTATCCCAACCTTTTTTAAAAGTTACCTT
* * * * * *
4245019 AGACATGGTCTATCCCAACCTTTTTAAGGTTGCCTTAGACGAGTCTATTCCGACCTTTTTTAAAG
66 AGACATGGTCGATCCCAACCTTTTTAAGGTTGCATTAGACGAGTCTATCCCAACCGTTTTTAAAA
4245084 GTTGCCTTAGACATGG
131 GTTGCCTTAGACATGG
* * * * * ***
4245100 TCTATCCTAACCTGTTTAAGGTTGCCTTAGATAGGTCTATCCCAACCTTTTTTTATAGGTTGTTT
1 TCTATCCCAACCTGTTTAAGGTTGCCTTAAACAGGTCTATCCCAACC-TTTTTTAAAAGTTACCT
4245165 TAGACAAT-GTCGATCCCAACCTTTTTAAGGTTGCATTAGACG-GCTCTATCCCAACCGTTTTTA
65 TAGAC-ATGGTCGATCCCAACCTTTTTAAGGTTGCATTAGACGAG-TCTATCCCAACCGTTTTTA
* * *
4245228 AAAGTTGCCTTAAACAAGA
128 AAAGTTGCCTTAGACATGG
* ** * * * * * *
4245247 ACTATATCGACCT-TTTAATGTTGTCTTAGACAGGTTTATCACAACCTTTTT
1 TCTATCCCAACCTGTTTAAGGTTGCCTTAAACAGGTCTATCCCAACCTTTTT
4245298 CAAAGGTCGG
Statistics
Matches: 166, Mismatches: 29, Indels: 7
0.82 0.14 0.03
Matches are distributed among these distances:
145 5 0.03
146 71 0.43
147 88 0.53
148 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (146 bp):
TCTATCCCAACCTGTTTAAGGTTGCCTTAAACAGGTCTATCCCAACCTTTTTTAAAAGTTACCTT
AGACATGGTCGATCCCAACCTTTTTAAGGTTGCATTAGACGAGTCTATCCCAACCGTTTTTAAAA
GTTGCCTTAGACATGG
Found at i:4245330 original size:38 final size:38
Alignment explanation
Indices: 4245269--4245345 Score: 104
Period size: 38 Copynumber: 2.0 Consensus size: 38
4245259 TTTTAATGTT
*
4245269 GTCTTAGACAGGTTTATCACAA-CCTTTTTCAAAGGTCG
1 GTCTTAGACAGGTCTATCACAACCCTTTTT-AAAGGTCG
*
4245307 GTCTTA-ACTAGGTCTATCCCAACCCTTTTTAAAGGTCG
1 GTCTTAGAC-AGGTCTATCACAACCCTTTTTAAAGGTCG
4245345 G
1 G
4245346 CTTTGACTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 2 0.06
38 26 0.74
39 7 0.20
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (38 bp):
GTCTTAGACAGGTCTATCACAACCCTTTTTAAAGGTCG
Found at i:4246654 original size:39 final size:39
Alignment explanation
Indices: 4246595--4246871 Score: 446
Period size: 39 Copynumber: 7.1 Consensus size: 39
4246585 ATGCAAAACA
*
4246595 CTGGAAATGTATCCGGGCTAAAAACCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
* *
4246634 CTAGAAATGTATCCGTGCTAAAGACCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
* * * *
4246673 TTGGAAATGTATCTGGGCTAAAGTCCCGCAGGCTTCATG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
4246712 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
4246751 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
* *
4246790 CTGGAAATGTATCAGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
* * *
4246829 CTGGAAATGTATCCGAGCTAAAGTCCCGCAGGCTTTGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
4246868 CTGG
1 CTGG
4246872 TAATATAATT
Statistics
Matches: 220, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 220 1.00
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.23
Consensus pattern (39 bp):
CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
Found at i:4250741 original size:40 final size:40
Alignment explanation
Indices: 4250696--4250863 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
4250686 CGGAATATAA
4250696 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
4250736 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
4250776 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * * *
4250816 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
4250856 CCGGATAT
1 CCGGATAT
4250864 CATTCAATTT
Statistics
Matches: 107, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 106 0.99
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:4255569 original size:29 final size:29
Alignment explanation
Indices: 4255527--4255656 Score: 192
Period size: 29 Copynumber: 4.5 Consensus size: 29
4255517 GACAAGATTG
4255527 GCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATATATA
* *
4255556 GCACTAAGTGTGCGAGTTTG--ATTATATA
1 GCACTAAGTGTGCGAG-CTGAAAATATATA
4255584 GCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATATATA
* *
4255613 GCACTAAGTGTGCGAGCTGAAAATTACATG
1 GCACTAAGTGTGCGAGCTGAAAA-TATATA
4255643 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
4255657 GATTCACTAT
Statistics
Matches: 91, Mismatches: 6, Indels: 7
0.88 0.06 0.07
Matches are distributed among these distances:
27 2 0.02
28 23 0.25
29 46 0.51
30 20 0.22
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (29 bp):
GCACTAAGTGTGCGAGCTGAAAATATATA
Found at i:4255656 original size:59 final size:57
Alignment explanation
Indices: 4255525--4255656 Score: 203
Period size: 57 Copynumber: 2.3 Consensus size: 57
4255515 GTGACAAGAT
* *
4255525 TGGCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAGTTTGATTATA
1 TGGCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAGTCTGATTACA
*
4255582 TAGCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAG-CTGAAAATTACA
1 TGGCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAGTCTG---ATTACA
4255641 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
4255657 GATTCACTAT
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
56 2 0.03
57 46 0.68
59 20 0.29
ACGTcount: A:0.33, C:0.14, G:0.27, T:0.27
Consensus pattern (57 bp):
TGGCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAGTCTGATTACA
Found at i:4263555 original size:29 final size:29
Alignment explanation
Indices: 4263513--4263642 Score: 192
Period size: 29 Copynumber: 4.5 Consensus size: 29
4263503 GACAAGATTG
4263513 GCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATATATA
* *
4263542 GCACTAAGTGTGCGAGTTTG--ATTATATA
1 GCACTAAGTGTGCGAG-CTGAAAATATATA
4263570 GCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATATATA
* *
4263599 GCACTAAGTGTGCGAGCTGAAAATTACATG
1 GCACTAAGTGTGCGAGCTGAAAA-TATATA
4263629 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
4263643 GATTCACTAT
Statistics
Matches: 91, Mismatches: 6, Indels: 7
0.88 0.06 0.07
Matches are distributed among these distances:
27 2 0.02
28 23 0.25
29 46 0.51
30 20 0.22
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (29 bp):
GCACTAAGTGTGCGAGCTGAAAATATATA
Found at i:4263642 original size:59 final size:57
Alignment explanation
Indices: 4263511--4263642 Score: 203
Period size: 57 Copynumber: 2.3 Consensus size: 57
4263501 GTGACAAGAT
* *
4263511 TGGCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAGTTTGATTATA
1 TGGCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAGTCTGATTACA
*
4263568 TAGCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAG-CTGAAAATTACA
1 TGGCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAGTCTG---ATTACA
4263627 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
4263643 GATTCACTAT
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
56 2 0.03
57 46 0.68
59 20 0.29
ACGTcount: A:0.33, C:0.14, G:0.27, T:0.27
Consensus pattern (57 bp):
TGGCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAGTCTGATTACA
Found at i:4266836 original size:39 final size:39
Alignment explanation
Indices: 4266733--4266887 Score: 194
Period size: 39 Copynumber: 4.1 Consensus size: 39
4266723 AAGCAAGACA
* *
4266733 CTGGAAATGTATCTGGGCTAAAAACCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
* **
4266772 CT--AGA--TA-CATGGCTAAAGACCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
*
4266806 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
* * *
4266845 CTGGAAATGTATCCGAGCTAAAGTCCCGCAGGCTTTGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
4266884 CTGG
1 CTGG
4266888 TAATATAATT
Statistics
Matches: 101, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
34 26 0.26
35 2 0.02
36 2 0.02
37 2 0.02
38 2 0.02
39 67 0.66
ACGTcount: A:0.23, C:0.25, G:0.29, T:0.23
Consensus pattern (39 bp):
CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
Found at i:4284674 original size:30 final size:30
Alignment explanation
Indices: 4284638--4284709 Score: 126
Period size: 30 Copynumber: 2.4 Consensus size: 30
4284628 AATCGGAAGT
4284638 TTTGGCACTAAGTGTGCGATTTAAACTAGC
1 TTTGGCACTAAGTGTGCGATTTAAACTAGC
*
4284668 TTTGGCAATAAGTGTGCGATTTAAACTAGC
1 TTTGGCACTAAGTGTGCGATTTAAACTAGC
4284698 TTTGGCTACTAA
1 TTTGGC-ACTAA
4284710 AGGCACAAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 35 0.90
31 4 0.10
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (30 bp):
TTTGGCACTAAGTGTGCGATTTAAACTAGC
Found at i:4292053 original size:30 final size:30
Alignment explanation
Indices: 4292017--4292088 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 30
4292007 AATCGAAAGT
4292017 TTTGGCACTAAGTGTGCGATTTAAACTAGC
1 TTTGGCACTAAGTGTGCGATTTAAACTAGC
4292047 TTTGGCACTAAGTGTGCGATTTAAACTAGC
1 TTTGGCACTAAGTGTGCGATTTAAACTAGC
4292077 TTTGGCTACTAA
1 TTTGGC-ACTAA
4292089 AGGCACTAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 36 0.88
31 5 0.12
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (30 bp):
TTTGGCACTAAGTGTGCGATTTAAACTAGC
Found at i:4292644 original size:22 final size:22
Alignment explanation
Indices: 4292601--4292644 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
4292591 AAATCAGACT
***
4292601 TTTAGCGGCGTTTTTTTTTGCC
1 TTTAGCGGCGTTTTTAAGTGCC
4292623 TTTAGCGGCGTTTTTAAGTGCC
1 TTTAGCGGCGTTTTTAAGTGCC
4292645 GCAAAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.18, G:0.25, T:0.48
Consensus pattern (22 bp):
TTTAGCGGCGTTTTTAAGTGCC
Found at i:4296628 original size:476 final size:477
Alignment explanation
Indices: 4295736--4297072 Score: 2478
Period size: 476 Copynumber: 2.8 Consensus size: 477
4295726 ATGTTATGTG
* *
4295736 AGTTATAACTTTTAAAGACATTTAAAAATATTAAATATTAAAATCAAACATCATTAATATAAAAA
1 AGTTATAACTTTTAAAGACATTTAAAAATATTAAATATTAAAATCAAACATTATTAATATAACAA
*
4295801 AATAGTAATTTGAATATAATAATATCAAAAAAGAATCGTAATTTAATTTTTATAAGTAAATTAGA
66 AATAGTAATTTGAATATAATAATATCAAAAAAGAATCGTAATTTAATTTTTATAAGTAAATTGGA
*
4295866 AATAAATTAAGGTTATATAAATATTCAATAGCGATAGAACTTTTTTCAAGTCTTTTTGAATTTTT
131 AATAAATTAAGGTTATATAAATATTCAATAGCGATAGAACTTTTTTCAATTCTTTTTGAATTTTT
4295931 TAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAGCTCGATAT
196 TAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAGCTCGATAT
*
4295996 AAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTAAATCTTTAAAATATTTAAAATAAGGAATG
261 AAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGAATG
*
4296061 GACAAGCAATCTACATATATGGTAATAAAATTAATTCATACTTATTCATACTTAAATTGAATCAA
326 GACAAGCAAGCTACATATATGGTAATAAAATTAATTCATACTTATTCATACTTAAATTGAATCAA
4296126 ATAATAATTAAGTTGAACCAAAATAT-AAAACTTATTCATACTTATTCATACTTCAAATAATAAT
391 ATAATAATTAAGTTGAACCAAAATATAAAAACTTATTCATACTTATTCATACTTCAAATAATAAT
4296190 TAATACTGTTTTGATAAAAATT
456 TAATACTGTTTTGATAAAAATT
*
4296212 AGTTATAACTTTTAAAGACATTTAAAAATATTAAAAATTAAAATCAAACATTATTAATATAACAA
1 AGTTATAACTTTTAAAGACATTTAAAAATATTAAATATTAAAATCAAACATTATTAATATAACAA
*
4296277 AATAGTAATTTGAATATAATAATATCAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGA
66 AATAGTAATTTGAATATAATAATATCAAAAAAGAATCGTAATTTAATTTTTATAAGTAAATTGGA
*
4296342 AATAAATTAAGGTTATATAAATATTCAATAGCGACAGAACTTTTTTCAATTCTTTTTGAATTTTT
131 AATAAATTAAGGTTATATAAATATTCAATAGCGATAGAACTTTTTTCAATTCTTTTTGAATTTTT
*
4296407 TAAGATTCATCATACGTGGTGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAGCTCGATAT
196 TAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAGCTCGATAT
4296472 AAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGAATG
261 AAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGAATG
* * *
4296537 GGCAAGCAAGCTACATATACGGTAATAAAATTAATTCATACTTATTCATACTTAAGTTGAATCAA
326 GACAAGCAAGCTACATATATGGTAATAAAATTAATTCATACTTATTCATACTTAAATTGAATCAA
4296602 ATAATAATTAAGTTGAACCAAAATATAAAAACTTATTCATACTTATTCATACTTCAAATAATAAT
391 ATAATAATTAAGTTGAACCAAAATATAAAAACTTATTCATACTTATTCATACTTCAAATAATAAT
*
4296667 TAATATTGTTTTGATAAAAATT
456 TAATACTGTTTTGATAAAAATT
*
4296689 AGTTATAACTTTTAAAGACATTTAAAAACATTAAATATTAAAATCAAACATTATTAATATAACAA
1 AGTTATAACTTTTAAAGACATTTAAAAATATTAAATATTAAAATCAAACATTATTAATATAACAA
*
4296754 AATAGTAATTTGAATATAATAATATCAAAAAAGAATCATAATTTAATTTTTATAAGTAAATTGGA
66 AATAGTAATTTGAATATAATAATATCAAAAAAGAATCGTAATTTAATTTTTATAAGTAAATTGGA
*
4296819 AATAAATTAAGGTTATATAAATATTCAATAACGATAGAACCTTTTTTCAATTCTTTTTGAATTTT
131 AATAAATTAAGGTTATATAAATATTCAATAGCGATAGAA-CTTTTTTCAATTCTTTTTGAATTTT
* *
4296884 TTAAGATTCATCATATGTGGCGTTGTTACACCTAGGGAGTATCCATTATATCTTGCAGCTCGATA
195 TTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAGCTCGATA
4296949 TAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGAAT
260 TAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGAAT
4297014 GGACAAGCAAGCTACATATATGGTAATAAAATTAATTCATACTTATTCATACTTCAAAT
325 GGACAAGCAAGCTACATATATGGTAATAAAATTAATTCATACTTATTCATACTT-AAAT
4297073 AATTAATACT
Statistics
Matches: 832, Mismatches: 26, Indels: 3
0.97 0.03 0.00
Matches are distributed among these distances:
476 403 0.48
477 222 0.27
478 204 0.25
479 3 0.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (477 bp):
AGTTATAACTTTTAAAGACATTTAAAAATATTAAATATTAAAATCAAACATTATTAATATAACAA
AATAGTAATTTGAATATAATAATATCAAAAAAGAATCGTAATTTAATTTTTATAAGTAAATTGGA
AATAAATTAAGGTTATATAAATATTCAATAGCGATAGAACTTTTTTCAATTCTTTTTGAATTTTT
TAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAGCTCGATAT
AAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGAATG
GACAAGCAAGCTACATATATGGTAATAAAATTAATTCATACTTATTCATACTTAAATTGAATCAA
ATAATAATTAAGTTGAACCAAAATATAAAAACTTATTCATACTTATTCATACTTCAAATAATAAT
TAATACTGTTTTGATAAAAATT
Found at i:4301441 original size:2 final size:2
Alignment explanation
Indices: 4301397--4301422 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4301387 ACCACTTTTC
4301397 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
4301423 TAAAATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4301455 original size:15 final size:15
Alignment explanation
Indices: 4301435--4301466 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4301425 AAATAATAAT
*
4301435 TTATATATATTTATC
1 TTATATACATTTATC
4301450 TTATATACATTTATC
1 TTATATACATTTATC
4301465 TT
1 TT
4301467 CTAAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATATACATTTATC
Found at i:4302553 original size:41 final size:41
Alignment explanation
Indices: 4302495--4302672 Score: 218
Period size: 41 Copynumber: 4.4 Consensus size: 41
4302485 GTTAAATGAC
*
4302495 TTTTAGCGGCGTTTTACCAAAAGCACCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
*
4302536 TTTTAGCGGCGTGTTACCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
* * * *
4302577 TCTTAGAGGCGTTTTACCAAAAGCGCCGCTATTGCTCT-AT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
* **
4302617 TTTTAGCGGCGTTTTTTACTAAAA-CGCCGCTGTTGCTCT-GT
1 TTTTAGCGGCG--TTTTACCAAAAGCGCCGCTAATGCTCTGGT
**
4302658 TTTTAATGGCGTTTT
1 TTTTAGCGGCGTTTT
4302673 TCTTAAAACA
Statistics
Matches: 121, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
39 4 0.03
40 10 0.08
41 97 0.80
42 10 0.08
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.36
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
Found at i:4302693 original size:40 final size:40
Alignment explanation
Indices: 4302605--4302704 Score: 103
Period size: 41 Copynumber: 2.5 Consensus size: 40
4302595 AAAAGCGCCG
* * * *
4302605 CTATTGCTCTATTTTTAGCGGCGTTTTTTACTAAAACGCCG
1 CTATTGCTCTGTTTTTAACGGCGTTTTTTA-TAAAACACCA
* * *
4302646 CTGTTGCTCTGTTTTTAATGGCGTTTTTCT-TAAAACACTA
1 CTATTGCTCTGTTTTTAACGGCGTTTTT-TATAAAACACCA
4302686 CTATTGCTCTGTATTTTAA
1 CTATTGCTCTGT-TTTTAA
4302705 AATTTTTGCG
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
40 18 0.37
41 30 0.61
42 1 0.02
ACGTcount: A:0.20, C:0.19, G:0.15, T:0.46
Consensus pattern (40 bp):
CTATTGCTCTGTTTTTAACGGCGTTTTTTATAAAACACCA
Found at i:4306299 original size:144 final size:144
Alignment explanation
Indices: 4305829--4306459 Score: 647
Period size: 144 Copynumber: 4.4 Consensus size: 144
4305819 ATCCAACTTG
** *
4305829 ACTTCATTGTACCTCTCTCTCAAAACAAATTGAGTGGTTTGATCCCTTCTTGTATTGGTAGTTTA
1 ACTTCATTGTACCTCT-TC-CAAAACAAATTGAGTGGTTCAATCCCTTCTTGTATTGGTAGATTA
* * *
4305894 TCAAAAATGCAGTATTTAAGACTTGGTTCTAATCTATTAGAAGGTCCTATTCCCCAAGAAATTTG
64 TCCAAAATGCAGTACTTAAGACTTGATTCTAATCTATTAGAAGGTCCTATTCCCCAAGAAATTTG
* * *
4305959 TGATTTGGGAAATTTA
129 TAATTTCGCAAATTTA
* * * * * *
4305975 ACTTCATTAG-GCCTCTACCAAAACAAATTGAATGGTTCAGTCCCTTCTTGTCTTGGTA-AGTTG
1 ACTTCATT-GTACCTCTTCCAAAACAAATTGAGTGGTTCAATCCCTTCTTGTATTGGTAGA-TTA
* * * ***
4306038 TCCAAATTGCA-TACTTTAAGACTTGACTC-AAACTATTAGAAGGTCCTATTCTTGAAGAAATTT
64 TCCAAAATGCAGTAC-TTAAGACTTGATTCTAATCTATTAGAAGGTCCTATTCCCCAAGAAATTT
* * *
4306101 GTGACTTAGCAAATTTA
128 GTAATTTCGCAAATTTA
* * * * * * *
4306118 ACTTCATT-AAGCCTCTACCAAAACAAATTGAATGGTTCAATCCCTTTTTGTCTTGGTACATTGT
1 ACTTCATTGTA-CCTCTTCCAAAACAAATTGAGTGGTTCAATCCCTTCTTGTATTGGTAGATTAT
* * *
4306182 CCAAATTGGA-TACCTTACA-ACTTCATTC-AACTCTATTAGAAGGTCCTATTCCCCAA-AAATT
65 CCAAAATGCAGTA-CTTA-AGACTTGATTCTAA-TCTATTAGAAGGTCCTATTCCCCAAGAAA-T
4306243 TTGTAATTTCGCAAATTTA
126 TTGTAATTTCGCAAATTTA
* * *
4306262 ACTTTATTGTACCTCTTCCAAAACAAATTGAGTGGTTCAATCCTTTCTTGTATTGGTAGTTTAT-
1 ACTTCATTGTACCTCTTCCAAAACAAATTGAGTGGTTCAATCCCTTCTTGTATTGGTAGATTATC
* * * *
4306326 CAAAGATGCAGTACTTCAGCCTTGGTTCTAATCTATTAAAAGGTCCTATTCCCCAAGAAATTTGT
66 CAAA-ATGCAGTACTTAAGACTTGATTCTAATCTATTAGAAGGTCCTATTCCCCAAGAAATTTGT
*
4306391 AA-TTCAGAAAATTTA
130 AATTTC-GCAAATTTA
* * * *
4306406 ACTTTATTGTACCTC-TCCGAAAACAAATTGAGTTGTTCAATCCCATCATGTATT
1 ACTTCATTGTACCTCTTCC-AAAACAAATTGAGTGGTTCAATCCCTTCTTGTATT
4306460 TTCAATTTAT
Statistics
Matches: 411, Mismatches: 56, Indels: 38
0.81 0.11 0.08
Matches are distributed among these distances:
143 140 0.34
144 248 0.60
145 9 0.02
146 13 0.03
147 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (144 bp):
ACTTCATTGTACCTCTTCCAAAACAAATTGAGTGGTTCAATCCCTTCTTGTATTGGTAGATTATC
CAAAATGCAGTACTTAAGACTTGATTCTAATCTATTAGAAGGTCCTATTCCCCAAGAAATTTGTA
ATTTCGCAAATTTA
Found at i:4311120 original size:12 final size:13
Alignment explanation
Indices: 4311093--4311125 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
4311083 CAAAATATTG
4311093 AATTTGTTTGTAAA
1 AATTTG-TTGTAAA
4311107 AATTTGTT-TAAA
1 AATTTGTTGTAAA
4311119 AATTTGT
1 AATTTGT
4311126 ACAATTTCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.58
13 2 0.11
14 6 0.32
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (13 bp):
AATTTGTTGTAAA
Found at i:4311728 original size:38 final size:41
Alignment explanation
Indices: 4311666--4311753 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 41
4311656 TAAAAAAGAT
*
4311666 TTATATTAAAAAATACTACCATAAATATAATAAATG-TTTTA
1 TTATATTAAAAAATACTACAATAAATATAATAAA-GATTTTA
* *
4311707 TTATATTAAAAAA-AC-A-AATAAATGTACTAAAGATTTTA
1 TTATATTAAAAAATACTACAATAAATATAATAAAGATTTTA
*
4311745 TTTTATTAA
1 TTATATTAA
4311754 TTAATTTTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
37 1 0.02
38 25 0.60
39 1 0.02
40 2 0.05
41 13 0.31
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (41 bp):
TTATATTAAAAAATACTACAATAAATATAATAAAGATTTTA
Found at i:4312794 original size:8 final size:8
Alignment explanation
Indices: 4312772--4312805 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
4312762 GGGCCTGTGA
*
4312772 AATAGAAT
1 AATAAAAT
*
4312780 AAAAAAAT
1 AATAAAAT
4312788 AATAAAAT
1 AATAAAAT
4312796 AATAAAAT
1 AATAAAAT
4312804 AA
1 AA
4312806 ATTTAATGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (8 bp):
AATAAAAT
Found at i:4314352 original size:18 final size:18
Alignment explanation
Indices: 4314329--4314364 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
4314319 ATCCTTTATT
4314329 ATTTTTATATTGT-TTTAA
1 ATTTTTAT-TTGTATTTAA
4314347 ATTTTTATTTGTATTTAA
1 ATTTTTATTTGTATTTAA
4314365 TCTTATCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (18 bp):
ATTTTTATTTGTATTTAA
Found at i:4314656 original size:9 final size:9
Alignment explanation
Indices: 4314642--4314666 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
4314632 AATGTATGTA
4314642 TATTTACGT
1 TATTTACGT
4314651 TATTTACGT
1 TATTTACGT
4314660 TATTTAC
1 TATTTAC
4314667 AATTATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.12, G:0.08, T:0.56
Consensus pattern (9 bp):
TATTTACGT
Found at i:4326154 original size:44 final size:44
Alignment explanation
Indices: 4326024--4326619 Score: 628
Period size: 44 Copynumber: 13.6 Consensus size: 44
4326014 ATAGATTACT
*
4326024 GATAGCAGATTTGGCGTCTTTGTATTGTCAGAGAGCAGATCGAA
1 GATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA
* * * * * * *
4326068 GATAACAGGTTTGGTGTCTCTGTATT-ACTAAAGAGTAAATCGAA
1 GATAGCAGATTTGGCGTCTCTGTATTGTC-AGAGAGCAGATCGAA
* * * *
4326112 GATAACAGGTTTGGCGTCTCTGTATTATCAGGGAGCAGATCGAA
1 GATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA
* * * * *
4326156 GATAGTAGATTTGACATCTCTGTATGGTCAGAAAGCAGATC-ACCA
1 GATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGA--A
* *
4326201 -ATAGCAGATTTGGCGTCTCTATATTGGCAGAGAGCAGAT-GAAA
1 GATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCG-AA
* *
4326244 GATAGTAGGTTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA
1 GATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA
* *
4326288 GATAGCAGATTTGGCATTTC-GTATTGTCAGAGAGCAGATCGAA
1 GATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA
* * * *
4326331 GATAGTAGATTTGGCATCTCTATATTGTCAAAGAGCAGATCGAA
1 GATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA
*
4326375 GATAGTAGATTTGGCGTCTCTGT-TTGTCAGAGAGCAGATCGAA
1 GATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA
*
4326418 GATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCAAA
1 GATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA
* *
4326462 GATAGTAGATTTGGCGTCTCTGTATTGTCAAAGAGCAGATCGAA
1 GATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA
* * * * * * * * * * *
4326506 GAAAGCACATATAGCATTTCTTTATTGACAGAAAGTAGATCAAA
1 GATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA
* * * * * * * * * *
4326550 GAAAGCACATATAGCATTTCTGTATTGACAGAAAGTAGATCAAA
1 GATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA
* *
4326594 GATAGCTGATTTGGTGTCTCTGTATT
1 GATAGCAGATTTGGCGTCTCTGTATT
4326620 AGGCGGGGTG
Statistics
Matches: 470, Mismatches: 72, Indels: 20
0.84 0.13 0.04
Matches are distributed among these distances:
43 85 0.18
44 381 0.81
45 4 0.01
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (44 bp):
GATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA
Found at i:4328166 original size:29 final size:29
Alignment explanation
Indices: 4328120--4328199 Score: 89
Period size: 29 Copynumber: 2.9 Consensus size: 29
4328110 ACGCTTTATC
4328120 ATATATA-TATA-TA-TATATTATTTT-A
1 ATATATATTATATTATTATATTATTTTCA
* *
4328145 ATATATATTTTATTCATTATATCATTTTCA
1 ATATATATTATATT-ATTATATTATTTTCA
*
4328175 TTATATATTATATTATTAT-TTATTT
1 ATATATATTATATTATTATATTATTT
4328200 ATTACTATGT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
25 7 0.16
26 3 0.07
27 1 0.02
28 6 0.13
29 15 0.33
30 13 0.29
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (29 bp):
ATATATATTATATTATTATATTATTTTCA
Found at i:4330788 original size:15 final size:15
Alignment explanation
Indices: 4330768--4330799 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
4330758 TAAAAATTTG
4330768 GTCCGAAGGGTACTT
1 GTCCGAAGGGTACTT
4330783 GTCCGAAGGGTACTT
1 GTCCGAAGGGTACTT
4330798 GT
1 GT
4330800 ACCTTTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (15 bp):
GTCCGAAGGGTACTT
Found at i:4331457 original size:27 final size:29
Alignment explanation
Indices: 4331427--4331496 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
4331417 AAATAAAGGT
* *
4331427 TATAAAAACTA-TTAAA-TTTATTAAAAA
1 TATAAAAAATATTTAAATTTTAGTAAAAA
4331454 TATAAAAAATATTTAAATTTTAGTAAAAA
1 TATAAAAAATATTTAAATTTTAGTAAAAA
4331483 T-TAGAAAAA-ATTTA
1 TATA-AAAAATATTTA
4331497 TAAAAATCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
27 10 0.26
28 12 0.32
29 16 0.42
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (29 bp):
TATAAAAAATATTTAAATTTTAGTAAAAA
Found at i:4338382 original size:3 final size:3
Alignment explanation
Indices: 4338374--4338435 Score: 108
Period size: 3 Copynumber: 20.7 Consensus size: 3
4338364 ACTTTAAGAG
4338374 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4338422 TTAA -AA TAA TAA TA
1 -TAA TAA TAA TAA TA
4338436 CTTGACATGT
Statistics
Matches: 57, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
3 52 0.91
4 3 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:4339684 original size:21 final size:22
Alignment explanation
Indices: 4339655--4339699 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
4339645 CTAAGCATAC
*
4339655 AATTATAAATTTG-GTAAATGA
1 AATTATAAACTTGAGTAAATGA
*
4339676 AATTTTAAACTTGAAGTAAATGA
1 AATTATAAACTTG-AGTAAATGA
4339699 A
1 A
4339700 TATCGTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 11 0.55
23 9 0.45
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (22 bp):
AATTATAAACTTGAGTAAATGA
Found at i:4340248 original size:32 final size:32
Alignment explanation
Indices: 4340212--4340278 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
4340202 TATTAGTAAA
*
4340212 TTTCTCTATTTGGTCACCCAACTAT-TTAATTT
1 TTTCT-TATTTGGCCACCCAACTATCTTAATTT
* * *
4340244 TTTCTTTTTTGGCCACCCATCTATCTTGATTT
1 TTTCTTATTTGGCCACCCAACTATCTTAATTT
4340276 TTT
1 TTT
4340279 TGGTATTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 16 0.53
32 14 0.47
ACGTcount: A:0.16, C:0.22, G:0.07, T:0.54
Consensus pattern (32 bp):
TTTCTTATTTGGCCACCCAACTATCTTAATTT
Found at i:4343641 original size:15 final size:15
Alignment explanation
Indices: 4343621--4343649 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4343611 GTATTTTATA
4343621 ATTTTTAATAATTTT
1 ATTTTTAATAATTTT
4343636 ATTTTTAATAATTT
1 ATTTTTAATAATTT
4343650 ACTTGATTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
ATTTTTAATAATTTT
Found at i:4344634 original size:85 final size:85
Alignment explanation
Indices: 4344491--4344664 Score: 267
Period size: 85 Copynumber: 2.0 Consensus size: 85
4344481 AACGCTGCTA
* * * * *
4344491 AAAGTCAGGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGGTCATGACCTTTAGTGGCG
1 AAAGTCAGAACCTTTAGCGACGCTTTTCCCACAAACGCCGCCAAAGGTCAGGACCTTTAGCGGCG
* *
4344556 CTTTTCCCACAAACGCCGCC
66 CTTTTCCAAAAAACGCCGCC
*
4344576 AAAGTCAGAACCTTTAGCGACGCTTTTCTCACAAACGCCGCCAAAGGTCAGGACCTTTAGCGGCG
1 AAAGTCAGAACCTTTAGCGACGCTTTTCCCACAAACGCCGCCAAAGGTCAGGACCTTTAGCGGCG
*
4344641 CTTTTCCAAAAAATGCCGCC
66 CTTTTCCAAAAAACGCCGCC
4344661 AAAG
1 AAAG
4344665 GTCATAAAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
85 80 1.00
ACGTcount: A:0.27, C:0.31, G:0.21, T:0.21
Consensus pattern (85 bp):
AAAGTCAGAACCTTTAGCGACGCTTTTCCCACAAACGCCGCCAAAGGTCAGGACCTTTAGCGGCG
CTTTTCCAAAAAACGCCGCC
Found at i:4344659 original size:43 final size:43
Alignment explanation
Indices: 4344480--4344668 Score: 263
Period size: 43 Copynumber: 4.4 Consensus size: 43
4344470 GTTTATTTGA
* * *
4344480 AAACGCTGCTAAAAGTCAGGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCCAAAGGTCAGGACCTTTAGCGGCGCTTTTCCCAC
* * *
4344523 AAACGCCGCTAAAGGTCATGACCTTTAGTGGCGCTTTTCCCAC
1 AAACGCCGCCAAAGGTCAGGACCTTTAGCGGCGCTTTTCCCAC
* * *
4344566 AAACGCCGCCAAA-GTCAGAACCTTTAGCGACGCTTTTCTCAC
1 AAACGCCGCCAAAGGTCAGGACCTTTAGCGGCGCTTTTCCCAC
* *
4344608 AAACGCCGCCAAAGGTCAGGACCTTTAGCGGCGCTTTTCCAAA
1 AAACGCCGCCAAAGGTCAGGACCTTTAGCGGCGCTTTTCCCAC
*
4344651 AAATGCCGCCAAAGGTCA
1 AAACGCCGCCAAAGGTCA
4344669 TAAAAATTAA
Statistics
Matches: 129, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
42 37 0.29
43 92 0.71
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.21
Consensus pattern (43 bp):
AAACGCCGCCAAAGGTCAGGACCTTTAGCGGCGCTTTTCCCAC
Found at i:4349882 original size:23 final size:23
Alignment explanation
Indices: 4349856--4349918 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
4349846 TAAAAAATGC
4349856 TAATACAATTACATATAAAATTT
1 TAATACAATTACATATAAAATTT
*
4349879 TAATA-AATATAAAT-TAAAAATTT
1 TAATACAAT-TACATAT-AAAATTT
* *
4349902 AAATACAAGTACATATA
1 TAATACAATTACATATA
4349919 TAGGATATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
22 4 0.12
23 25 0.78
24 3 0.09
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.35
Consensus pattern (23 bp):
TAATACAATTACATATAAAATTT
Found at i:4350410 original size:21 final size:22
Alignment explanation
Indices: 4350384--4350445 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 22
4350374 TCTAAACTCT
4350384 AAACCCTTAACCCTT-AACCCC
1 AAACCCTTAACCCTTAAACCCC
*
4350405 AAACCCTT-ACACCTTAAACTCC
1 AAACCCTTAAC-CCTTAAACCCC
*
4350427 -AA-CCTTAACCCCTAAACCC
1 AAACCCTTAACCCTTAAACCC
4350446 TAAATTATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
20 14 0.40
21 16 0.46
22 5 0.14
ACGTcount: A:0.35, C:0.45, G:0.00, T:0.19
Consensus pattern (22 bp):
AAACCCTTAACCCTTAAACCCC
Found at i:4350535 original size:21 final size:21
Alignment explanation
Indices: 4350509--4350593 Score: 89
Period size: 21 Copynumber: 3.9 Consensus size: 21
4350499 ACTCCTAAAC
*
4350509 CTTAAACCCTAAACCATATAT
1 CTTAAACCATAAACCATATAT
* *
4350530 CTTAAACCATAGTTAACTCAAAAAT
1 CTTAAACCATA---AAC-CATATAT
* *
4350555 CTTAAACCCTAAACTATATAT
1 CTTAAACCATAAACCATATAT
4350576 CTTAAACCATAAACCATA
1 CTTAAACCATAAACCATA
4350594 AACTATAATG
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
21 30 0.59
22 3 0.06
24 3 0.06
25 15 0.29
ACGTcount: A:0.46, C:0.25, G:0.01, T:0.28
Consensus pattern (21 bp):
CTTAAACCATAAACCATATAT
Found at i:4350546 original size:46 final size:46
Alignment explanation
Indices: 4350493--4350586 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 46
4350483 CTTCAAATAC
**
4350493 TAGTTAACTCCTAAACCTTAAACCCTAAACCATATATCTTAAACCA
1 TAGTTAACTCAAAAACCTTAAACCCTAAACCATATATCTTAAACCA
* *
4350539 TAGTTAACTCAAAAATCTTAAACCCTAAACTATATATCTTAAACCA
1 TAGTTAACTCAAAAACCTTAAACCCTAAACCATATATCTTAAACCA
4350585 TA
1 TA
4350587 AACCATAAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.44, C:0.24, G:0.02, T:0.30
Consensus pattern (46 bp):
TAGTTAACTCAAAAACCTTAAACCCTAAACCATATATCTTAAACCA
Found at i:4350819 original size:41 final size:41
Alignment explanation
Indices: 4350758--4351140 Score: 621
Period size: 41 Copynumber: 9.4 Consensus size: 41
4350748 GTTATATGAC
*
4350758 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
*
4350799 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
4350840 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGG-
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
*
4350880 TTTTAGCGGCATTTTTCCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
*
4350921 TTTTAGCGGCATTTTTCCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
4350962 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
** **
4351003 TTTTAGTAGCGTTTTGACAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
4351044 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCT-GT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
* *
4351084 TTTTAGCGGCGTTTTTTACTAAAA-CGCCGCTATTGCTCT-GT
1 TTTTAGCGGCG-TTTTT-CCAAAAGCGCCGCTAATGCTCTGGT
*
4351125 TTTTAGTGGCGTTTTT
1 TTTTAGCGGCGTTTTT
4351141 GGTAAAACGC
Statistics
Matches: 324, Mismatches: 15, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
40 57 0.18
41 262 0.81
42 5 0.02
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
Found at i:4350975 original size:122 final size:122
Alignment explanation
Indices: 4350758--4351156 Score: 624
Period size: 122 Copynumber: 3.3 Consensus size: 122
4350748 GTTATATGAC
*
4350758 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACCAAAAGC
1 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTTCCAAAAGC
4350823 GCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGG
66 GCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGG
* * *
4350880 TTTTAGCGGCATTTTTCCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCATTTTTCCAAAAGC
1 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTTCCAAAAGC
4350945 GCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGG
66 GCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGG
** *
4351002 TTTTTAGTAGCGTTTTGACAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTTCCAAAAG
1 -TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTTCCAAAAG
* * *
4351067 CGCCGCTAATGCTCT-GTTTTTAGCGGCGTTTTTTACTAAAA-CGCCGCTATTGCTCTGT
65 CGCCGCTAATGCTCTGGTTTTTAGCGGCG-TTTTT-CCAAAAGCGCCGCTAATGCTCTGG
* **
4351125 TTTTAGTGGCGTTTTTGGTAAAA-CGCCGCTAA
1 TTTTAGCGGCG-TTTTGCCAAAAGCGCCGCTAA
4351157 AGCCCTATTT
Statistics
Matches: 257, Mismatches: 16, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
122 150 0.58
123 102 0.40
124 5 0.02
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.35
Consensus pattern (122 bp):
TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTTCCAAAAGC
GCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGG
Found at i:4374770 original size:15 final size:16
Alignment explanation
Indices: 4374741--4374772 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4374731 CAATTAGTTT
4374741 TGAAAATGTTTTTTTA
1 TGAAAATGTTTTTTTA
4374757 TGAAAATGTTTTTTTA
1 TGAAAATGTTTTTTTA
4374773 CTAACTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (16 bp):
TGAAAATGTTTTTTTA
Found at i:4375544 original size:15 final size:15
Alignment explanation
Indices: 4375502--4375549 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
4375492 TTATAAATGT
4375502 TTATTTGTTTTATT-
1 TTATTTGTTTTATTG
* *
4375516 ATATTT-TTAT-TTG
1 TTATTTGTTTTATTG
4375529 TTATTTGTTTTATTG
1 TTATTTGTTTTATTG
4375544 TTATTT
1 TTATTT
4375550 TCTTTCATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
12 2 0.07
13 8 0.30
14 8 0.30
15 9 0.33
ACGTcount: A:0.17, C:0.00, G:0.08, T:0.75
Consensus pattern (15 bp):
TTATTTGTTTTATTG
Found at i:4375550 original size:27 final size:28
Alignment explanation
Indices: 4375502--4375569 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 28
4375492 TTATAAATGT
*
4375502 TTATTTGTTTTATTATATTTTTATTT-G
1 TTATTTGTTTTATTATATTTTTATTTCA
* *
4375529 TTATTTGTTTTATTGT-TATTTTCTTTCA
1 TTATTTGTTTTATTATAT-TTTTATTTCA
4375557 TT-TTTGTTTTATT
1 TTATTTGTTTTATT
4375570 TTTGTTCTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
26 1 0.03
27 33 0.92
28 2 0.06
ACGTcount: A:0.15, C:0.03, G:0.07, T:0.75
Consensus pattern (28 bp):
TTATTTGTTTTATTATATTTTTATTTCA
Found at i:4375600 original size:18 final size:19
Alignment explanation
Indices: 4375577--4375616 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
4375567 ATTTTTGTTC
4375577 TCTTTTTACACTTT-TTTT
1 TCTTTTTACACTTTCTTTT
**
4375595 TCTTTTTATTCTTTCTTTT
1 TCTTTTTACACTTTCTTTT
4375614 TCT
1 TCT
4375617 CTCTGTTCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.75
Consensus pattern (19 bp):
TCTTTTTACACTTTCTTTT
Found at i:4377045 original size:92 final size:92
Alignment explanation
Indices: 4376875--4377067 Score: 226
Period size: 92 Copynumber: 2.1 Consensus size: 92
4376865 ATTGACTAAA
* *
4376875 CTGGCAGTTTTACTGCAACCTAACGGTATAGCGATTTACCGCATTGCGCTATACCACATGTACGT
1 CTGGCAGTTTTACTGCAACCTAACGGTATAGCGATTTACCGCATTGCACTATACCACATATACGT
***
4376940 TAGCTATGCTACGTACCATTAACTGAG
66 TAGCTAAAATACGTACCATTAACTGAG
* * ** * * *
4376967 CTGGTAGTTTTACTGCAATCTATTGGTATAGCGAATTT-TCGCATTGCACTGTACCGCATATACG
1 CTGGCAGTTTTACTGCAACCTAACGGTATAGCG-ATTTACCGCATTGCACTATACCACATATACG
* * *
4377031 TTAGCTAAAATACGTACTATTATCTGAT
65 TTAGCTAAAATACGTACCATTAACTGAG
*
4377059 CTAGCAGTT
1 CTGGCAGTT
4377068 CATATTGCAT
Statistics
Matches: 83, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
92 79 0.95
93 4 0.05
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (92 bp):
CTGGCAGTTTTACTGCAACCTAACGGTATAGCGATTTACCGCATTGCACTATACCACATATACGT
TAGCTAAAATACGTACCATTAACTGAG
Found at i:4377460 original size:25 final size:25
Alignment explanation
Indices: 4377426--4377511 Score: 109
Period size: 25 Copynumber: 3.4 Consensus size: 25
4377416 TATGCATCAT
4377426 ATTGACTGTTCGACTAAAATGTCTA
1 ATTGACTGTTCGACTAAAATGTCTA
* * * *
4377451 ATTGACTGTTTGATTGAAGTGTCTA
1 ATTGACTGTTCGACTAAAATGTCTA
* * *
4377476 ATTGACTGTTCAACTACAATGTCTG
1 ATTGACTGTTCGACTAAAATGTCTA
4377501 ATTGACTGTTC
1 ATTGACTGTTC
4377512 TACTGAAAGG
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.40
Consensus pattern (25 bp):
ATTGACTGTTCGACTAAAATGTCTA
Found at i:4378639 original size:2 final size:2
Alignment explanation
Indices: 4378634--4378659 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4378624 AAAAATATGA
4378634 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
4378660 GGTAGATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4380364 original size:11 final size:11
Alignment explanation
Indices: 4380348--4380372 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4380338 ATTAGTTAAC
4380348 TATAAAATAAT
1 TATAAAATAAT
4380359 TATAAAATAAT
1 TATAAAATAAT
4380370 TAT
1 TAT
4380373 TTAATTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TATAAAATAAT
Found at i:4381655 original size:2 final size:2
Alignment explanation
Indices: 4381648--4381678 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4381638 ATGAAATTTG
4381648 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4381679 TTTGAAAGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:4382746 original size:38 final size:38
Alignment explanation
Indices: 4382649--4382756 Score: 162
Period size: 38 Copynumber: 2.8 Consensus size: 38
4382639 GGCTTAAAGA
** *
4382649 CCCGCAGGCTTCGTGCTGGTAAAATATCCGGGTTAAAT
1 CCCGCAGGCTTCGTGCTGGTATTATATCCGGGATAAAT
4382687 CCCGCAGGCTTCGTGCTGGTATTATATCCGGGATAAAT
1 CCCGCAGGCTTCGTGCTGGTATTATATCCGGGATAAAT
* * *
4382725 CCCGCAGGCCTAGTGCTGGTATTATATTCGGG
1 CCCGCAGGCTTCGTGCTGGTATTATATCCGGG
4382757 CCTTCGTGCC
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 64 1.00
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.28
Consensus pattern (38 bp):
CCCGCAGGCTTCGTGCTGGTATTATATCCGGGATAAAT
Found at i:4382806 original size:43 final size:43
Alignment explanation
Indices: 4382728--4382903 Score: 257
Period size: 43 Copynumber: 4.1 Consensus size: 43
4382718 GATAAATCCC
* * *
4382728 GCAGGCCTAGTGCTGGT-ATTA-TATTCGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCTGGTGATGAGTATTCGGGCCTTCGTGCCTA
*
4382769 GCAGGCTTCGTGCTGGTGATGAGTATTCTGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCTGGTGATGAGTATTCGGGCCTTCGTGCCTA
* * *
4382812 GAAGGCTTCGTGCTGGTGATGTGTATTCGGGCCTTGGTGCCTA
1 GCAGGCTTCGTGCTGGTGATGAGTATTCGGGCCTTCGTGCCTA
* *
4382855 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCTGGTGATGAGTATTCGGGCCTTCGTGCCTA
4382898 GCAGGC
1 GCAGGC
4382904 GTAATGCCGG
Statistics
Matches: 122, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
41 15 0.12
42 3 0.02
43 104 0.85
ACGTcount: A:0.12, C:0.23, G:0.34, T:0.31
Consensus pattern (43 bp):
GCAGGCTTCGTGCTGGTGATGAGTATTCGGGCCTTCGTGCCTA
Found at i:4384525 original size:48 final size:48
Alignment explanation
Indices: 4384431--4384534 Score: 122
Period size: 48 Copynumber: 2.2 Consensus size: 48
4384421 TGTGCTAAGC
* * *
4384431 GTAAGACCTATCTGGGATAGGCATCGGCACAGCCCAGTGAGTGCTAGT
1 GTAAGACCTATCTGGGATAGGCATCAGCACAGCCCAGAGAGAGCTAGT
**
4384479 GTAAGACCTATC-GGGAATAGGCATCAGCAC-GGGCAGAGCAGAGCTAGT
1 GTAAGACCTATCTGGG-ATAGGCATCAGCACAGCCCAGAG-AGAGCTAGT
*
4384527 ATAAGACC
1 GTAAGACC
4384535 ATAGTTGGAC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
47 8 0.17
48 40 0.83
ACGTcount: A:0.30, C:0.22, G:0.31, T:0.17
Consensus pattern (48 bp):
GTAAGACCTATCTGGGATAGGCATCAGCACAGCCCAGAGAGAGCTAGT
Found at i:4390838 original size:21 final size:21
Alignment explanation
Indices: 4390812--4390852 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4390802 ATCTGCTCAA
* *
4390812 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
4390833 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
4390853 TCGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:4401452 original size:2 final size:2
Alignment explanation
Indices: 4401445--4401469 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4401435 ACAATGGTTA
4401445 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4401470 AATGTATTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4401672 original size:15 final size:15
Alignment explanation
Indices: 4401654--4401705 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
4401644 AATTGTTAAT
4401654 AATAAAATGATATAA
1 AATAAAATGATATAA
*
4401669 AATAAAATAATA-AA
1 AATAAAATGATATAA
4401683 TAATAAAAATGATATAA
1 -AAT-AAAATGATATAA
*
4401700 TATAAA
1 AATAAA
4401706 TAATGATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 2 0.06
15 17 0.55
16 10 0.32
17 2 0.06
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (15 bp):
AATAAAATGATATAA
Found at i:4401687 original size:30 final size:30
Alignment explanation
Indices: 4401651--4401709 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
4401641 ATAAATTGTT
4401651 AATAAT-AAAATGATATAAAATAAAATAATA
1 AATAATAAAAATGATATAAAAT-AAATAATA
*
4401681 AATAATAAAAATGATATAATATAAATAAT
1 AATAATAAAAATGATATAAAATAAATAAT
4401710 GATTTACATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 13 0.48
31 14 0.52
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (30 bp):
AATAATAAAAATGATATAAAATAAATAATA
Found at i:4403650 original size:17 final size:16
Alignment explanation
Indices: 4403628--4403670 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
4403618 ATTTTTCTTT
*
4403628 TAATAAAACAGAAGAAA
1 TAATAAAA-AAAAGAAA
4403645 TAATAATAAAAAAGAAA
1 TAATAA-AAAAAAGAAA
4403662 TAATAAAAA
1 TAATAAAAA
4403671 TAACCATATC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 3 0.12
17 19 0.79
18 2 0.08
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.16
Consensus pattern (16 bp):
TAATAAAAAAAAGAAA
Found at i:4403672 original size:20 final size:20
Alignment explanation
Indices: 4403629--4403673 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
4403619 TTTTTCTTTT
* *
4403629 AATAAAACAGAAGAAATAAT
1 AATAAAAAAGAAGAAATAAA
4403649 AATAAAAAAGAA-ATAATAAA
1 AATAAAAAAGAAGA-AATAAA
4403669 AATAA
1 AATAA
4403674 CCATATCACC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.16
Consensus pattern (20 bp):
AATAAAAAAGAAGAAATAAA
Found at i:4405680 original size:12 final size:12
Alignment explanation
Indices: 4405665--4405695 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
4405655 GATGTGTTAA
*
4405665 TGATCGGTTGTG
1 TGATCGGTCGTG
4405677 TGATCGGTCGTG
1 TGATCGGTCGTG
4405689 TGATCGG
1 TGATCGG
4405696 ACACAGGTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.13, G:0.42, T:0.35
Consensus pattern (12 bp):
TGATCGGTCGTG
Found at i:4408746 original size:79 final size:79
Alignment explanation
Indices: 4408518--4408840 Score: 303
Period size: 79 Copynumber: 4.0 Consensus size: 79
4408508 TATTTTCTTT
* *
4408518 CTCATTTTTGGCAATAAAATCAAAA--TGCAAT-AAATCCATTGAACGGCGGGAATCAATCCCGA
1 CTCATTTTTGGAAATAAAAT-AAAATTTGAAATAAAAT-CATTGAACGGCGGGAATCAATCCCGA
* *
4408580 CACGGATTCTATTTTA
64 AACGGATTTTATTTTA
* * ** *
4408596 CTCATTTTTGGAAATAAAACAAAATTTTAAATAAAATCATTGAACGGCAAGAATCAATCTCGAAA
1 CTCATTTTTGGAAATAAAATAAAATTTGAAATAAAATCATTGAACGGCGGGAATCAATCCCGAAA
4408661 CGGATTTTATTTTA
66 CGGATTTTATTTTA
* * *
4408675 CTCATTTTTGGAAATAAAATAAAATTTGGAATAAAATCGTTAAACGGCGGGAATCAATCCCGAAA
1 CTCATTTTTGGAAATAAAATAAAATTTGAAATAAAATCATTGAACGGCGGGAATCAATCCCGAAA
**
4408740 AAGATTTTA-TTTA
66 CGGATTTTATTTTA
* * ** *
4408753 CCTTTAATTTCCCATTTGGAAATAAAATCAAATTAATGGGATAAAATCCATTGAACGACGGGAAT
1 -C--TCA-TT----TTTGGAAATAAAATAAAATT--TGAAATAAAAT-CATTGAACGGCGGGAAT
* * *
4408818 AAATTCTGAAACGGATTTTATTT
55 CAATCCCGAAACGGATTTTATTT
4408841 ACTTTTAATT
Statistics
Matches: 200, Mismatches: 30, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
77 4 0.02
78 22 0.11
79 106 0.53
80 4 0.02
81 2 0.01
82 2 0.01
86 19 0.09
88 10 0.05
89 29 0.14
90 2 0.01
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (79 bp):
CTCATTTTTGGAAATAAAATAAAATTTGAAATAAAATCATTGAACGGCGGGAATCAATCCCGAAA
CGGATTTTATTTTA
Found at i:4408842 original size:89 final size:86
Alignment explanation
Indices: 4408681--4408851 Score: 216
Period size: 89 Copynumber: 2.0 Consensus size: 86
4408671 TTTACTCATT
* * *
4408681 TTTGGAAATAAAATAAAATTTGGAATAAAATCGTTAAACGGCGGGAATCAATCCCGAAAAAGATT
1 TTTGGAAATAAAATAAAATTTGGAATAAAATCATTAAACGACGGGAATAAATCCCGAAAAAGATT
4408746 TTATTTACCTTTAATTTCCCA
66 TTATTTACCTTTAATTTCCCA
* * * * * **
4408767 TTTGGAAATAAAATCAAATTAATGGGATAAAATCCATTGAACGACGGGAATAAATTCTGAAACGG
1 TTTGGAAATAAAATAAAATT--TGGAATAAAAT-CATTAAACGACGGGAATAAATCCCGAAAAAG
*
4408832 ATTTTATTTACTTTTAATTT
63 ATTTTATTTACCTTTAATTT
4408852 GGAAACAAAA
Statistics
Matches: 71, Mismatches: 11, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
86 19 0.27
88 10 0.14
89 42 0.59
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (86 bp):
TTTGGAAATAAAATAAAATTTGGAATAAAATCATTAAACGACGGGAATAAATCCCGAAAAAGATT
TTATTTACCTTTAATTTCCCA
Found at i:4409922 original size:259 final size:259
Alignment explanation
Indices: 4409432--4409951 Score: 925
Period size: 259 Copynumber: 2.0 Consensus size: 259
4409422 CCTTTTTCTA
*
4409432 TCATAGGAATGTTTGAAAATATGAAGAGGAAAAGGGAGACTTTTGAAAGTAGAAGAGTTTCGGTA
1 TCATAGGAATGTTTGAAAATACGAAGAGGAAAAGGGAGACTTTTGAAAGTAGAAGAGTTTCGGTA
*
4409497 AGAGGAAAAAATCAAAGATTATTTTGTGTGTAAAAACCCTTTAGAAATCACGGCCTTTTATCGGC
66 AGAGGAAAAAATCAAAGATTATTTTGTGTGTAAAAACCCTTTAGAAATCACGGCCTTTTATAGGC
4409562 ATGGAGATTGTTGGAATTTTGGAAAAATTATCCACAAAATCTACCATTAAATCAATTTGATTAAA
131 ATGGAGATTGTTGGAATTTTGGAAAAATTATCCACAAAATCTACCATTAAATCAATTTGATTAAA
4409627 AAATTTAATCAAATTTATTAGAATCAAATCAATAAGATAAGTATCCTTATATAAACAGATTATG
196 AAATTTAATCAAATTTATTAGAATCAAATCAATAAGATAAGTATCCTTATATAAACAGATTATG
*
4409691 TCATAGGAATGTTTGAAAATACGAAGAGGAAAAGGGAGACTTTTGAAAGTAGCAGAGTTTCGGTA
1 TCATAGGAATGTTTGAAAATACGAAGAGGAAAAGGGAGACTTTTGAAAGTAGAAGAGTTTCGGTA
*
4409756 AGAGGAAAAAATCAAAGATTATTTTGTGTGTAAAAACCCTTTAGAAATCATGGCCTTTTATAGGC
66 AGAGGAAAAAATCAAAGATTATTTTGTGTGTAAAAACCCTTTAGAAATCACGGCCTTTTATAGGC
* * *
4409821 ATGGAGATTGTTGGAATTTTGGAAAAATTATCTACAAAATTTGCCATTAAATCAATTTGATTAAA
131 ATGGAGATTGTTGGAATTTTGGAAAAATTATCCACAAAATCTACCATTAAATCAATTTGATT-AA
* * * *
4409886 AAAATTTAATTAAGTTTATTAGAATCAAAT-AATAAGATAAGTATCTTTATATAAGCAGATTATG
195 AAAATTTAATCAAATTTATTAGAATCAAATCAATAAGATAAGTATCCTTATATAAACAGATTATG
4409950 TC
1 TC
4409952 TGCAGAGGAA
Statistics
Matches: 249, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
259 219 0.88
260 30 0.12
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (259 bp):
TCATAGGAATGTTTGAAAATACGAAGAGGAAAAGGGAGACTTTTGAAAGTAGAAGAGTTTCGGTA
AGAGGAAAAAATCAAAGATTATTTTGTGTGTAAAAACCCTTTAGAAATCACGGCCTTTTATAGGC
ATGGAGATTGTTGGAATTTTGGAAAAATTATCCACAAAATCTACCATTAAATCAATTTGATTAAA
AAATTTAATCAAATTTATTAGAATCAAATCAATAAGATAAGTATCCTTATATAAACAGATTATG
Found at i:4410005 original size:69 final size:68
Alignment explanation
Indices: 4409900--4410038 Score: 260
Period size: 69 Copynumber: 2.0 Consensus size: 68
4409890 TTTAATTAAG
*
4409900 TTTATTAGAATCAAATAATAAGATAAGTATCTTTATATAAGCAGATTATGTCTGCAGAGGAAAAT
1 TTTATTAGAATCAAATAATAAGATAAGTATCCTTATATAAGCAGATTATGTCTGCAGAGGAAAAT
4409965 AAA
66 AAA
4409968 TTTATTAGAATCAAATCAATAAGATAAGTATCCTTATATAAGCAGATTATGTCTGCAGAGGAAAA
1 TTTATTAGAATCAAAT-AATAAGATAAGTATCCTTATATAAGCAGATTATGTCTGCAGAGGAAAA
4410033 TAAA
65 TAAA
4410037 TT
1 TT
4410039 CGTTTTGGGC
Statistics
Matches: 69, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
68 16 0.23
69 53 0.77
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.32
Consensus pattern (68 bp):
TTTATTAGAATCAAATAATAAGATAAGTATCCTTATATAAGCAGATTATGTCTGCAGAGGAAAAT
AAA
Found at i:4417105 original size:13 final size:14
Alignment explanation
Indices: 4417081--4417109 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
4417071 ACATGGGCAT
4417081 GTAGGCCCACATGG
1 GTAGGCCCACATGG
4417095 GTAGG-CCACATGG
1 GTAGGCCCACATGG
4417108 GT
1 GT
4417110 GTGTGAGCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.21, C:0.24, G:0.38, T:0.17
Consensus pattern (14 bp):
GTAGGCCCACATGG
Found at i:4417386 original size:27 final size:32
Alignment explanation
Indices: 4417314--4417386 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 32
4417304 GCCATATTTG
*
4417314 TATGATACATTGCATCGGAGTGGGGTTGGTGT
1 TATGATGCATTGCATCGGAGTGGGGTTGGTGT
*
4417346 TATGATGCATTGCATCGGGGTGGGGTTGGTGT
1 TATGATGCATTGCATCGGAGTGGGGTTGGTGT
4417378 TATGATGCA
1 TATGATGCA
4417387 GGACGTATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.18, C:0.10, G:0.38, T:0.34
Consensus pattern (32 bp):
TATGATGCATTGCATCGGAGTGGGGTTGGTGT
Found at i:4428772 original size:66 final size:69
Alignment explanation
Indices: 4428665--4428802 Score: 203
Period size: 66 Copynumber: 2.0 Consensus size: 69
4428655 CAGGGTTAAG
* *
4428665 TAGCACCACGAGATTGTAAATTATATTTCTTAAAGTAGCACCACTTCTG-TTT-TTTTCTTTTTA
1 TAGCACCACGAGATTGTAAATTATATTTCATAAAGTAGCACCACTACTGTTTTCTTTTCTTTTTA
4428728 AAAT
66 AAAT
*
4428732 TAGCACCACTAGA-TGTAAATTAT-TCTTCATAAAGTAGCACCACTACTGTTTTTCTTTTCTTTT
1 TAGCACCACGAGATTGTAAATTATAT-TTCATAAAGTAGCACCACTACTG-TTTTCTTTTCTTTT
4428795 TAAAAT
64 TAAAAT
4428801 TA
1 TA
4428803 CCATCTAAAT
Statistics
Matches: 64, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
65 1 0.02
66 31 0.48
67 12 0.19
68 3 0.05
69 17 0.27
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.43
Consensus pattern (69 bp):
TAGCACCACGAGATTGTAAATTATATTTCATAAAGTAGCACCACTACTGTTTTCTTTTCTTTTTA
AAAT
Found at i:4428792 original size:34 final size:33
Alignment explanation
Indices: 4428695--4428792 Score: 83
Period size: 34 Copynumber: 2.9 Consensus size: 33
4428685 TTATATTTCT
* *
4428695 TAAAGTAGCACCACTTCTGTTTTTTTCTT-TTTA
1 TAAAGTAGCACCACTACTGTTTTTTT-TTCTTCA
* * *** *
4428728 -AAATTAGCACCACTAGATGTAAATTATTCTTCA
1 TAAAGTAGCACCACTA-CTGTTTTTTTTTCTTCA
4428761 TAAAGTAGCACCACTACTGTTTTTCTTTTCTT
1 TAAAGTAGCACCACTACTGTTTTT-TTTTCTT
4428793 TTTAAAATTA
Statistics
Matches: 47, Mismatches: 14, Indels: 7
0.69 0.21 0.10
Matches are distributed among these distances:
32 15 0.32
33 12 0.26
34 20 0.43
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.44
Consensus pattern (33 bp):
TAAAGTAGCACCACTACTGTTTTTTTTTCTTCA
Found at i:4430109 original size:22 final size:22
Alignment explanation
Indices: 4430083--4430128 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
4430073 TGAAACTCCA
4430083 AAGACAAGAATATTAAATATTT
1 AAGACAAGAATATTAAATATTT
4430105 AAGACAAGAATATTAAATATTT
1 AAGACAAGAATATTAAATATTT
4430127 AA
1 AA
4430129 TAATATTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.57, C:0.04, G:0.09, T:0.30
Consensus pattern (22 bp):
AAGACAAGAATATTAAATATTT
Found at i:4430419 original size:50 final size:49
Alignment explanation
Indices: 4430325--4430420 Score: 133
Period size: 50 Copynumber: 2.0 Consensus size: 49
4430315 TAGTTACTTG
* *
4430325 ATTATGAAAAGTTATAAAATAGTTATTTAAATGTTATTAATTATTATTTA
1 ATTATGAAAAGTTATAAAATAATTATCTAAATGTTATT-ATTATTATTTA
* *
4430375 ATTATGAAAAGTTATAAAATAATTATCTAATTATT-TTATT-TTATTT
1 ATTATGAAAAGTTATAAAATAATTATCTAAATGTTATTATTATTATTT
4430421 TATTTGGTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
47 6 0.14
48 3 0.07
49 2 0.05
50 31 0.74
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (49 bp):
ATTATGAAAAGTTATAAAATAATTATCTAAATGTTATTATTATTATTTA
Found at i:4432777 original size:21 final size:20
Alignment explanation
Indices: 4432739--4432781 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
4432729 ATCCCAGTCC
4432739 CATGCATCAGATAATAACAA
1 CATGCATCAGATAATAACAA
4432759 CATGCATGCAG-TAAATAACAA
1 CATGCAT-CAGAT-AATAACAA
4432780 CA
1 CA
4432782 GTCAAACATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.49, C:0.21, G:0.12, T:0.19
Consensus pattern (20 bp):
CATGCATCAGATAATAACAA
Found at i:4432830 original size:25 final size:27
Alignment explanation
Indices: 4432793--4432845 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
4432783 TCAAACATGC
4432793 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
4432819 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
4432845 A
1 A
4432846 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:4434350 original size:26 final size:26
Alignment explanation
Indices: 4434319--4434426 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
4434309 TGAAATGCCC
*
4434319 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
4434345 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
4434371 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
4434397 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
4434423 ATCA
1 ATCA
4434427 ATTTGTATCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:4435625 original size:17 final size:17
Alignment explanation
Indices: 4435603--4435637 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
4435593 TATTCTACTT
*
4435603 TAATTTTATTATTGTTA
1 TAATTTTATTATTATTA
4435620 TAATTTTATTATTATTA
1 TAATTTTATTATTATTA
4435637 T
1 T
4435638 TATTATCATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (17 bp):
TAATTTTATTATTATTA
Found at i:4435631 original size:3 final size:3
Alignment explanation
Indices: 4435608--4435661 Score: 56
Period size: 3 Copynumber: 18.0 Consensus size: 3
4435598 TACTTTAATT
* * * *
4435608 TTA TTA TTG TTA TAA TT- TTA TTA TTA TTA TTA TTA TCA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4435655 TTTA TTA
1 -TTA TTA
4435662 GTGTATAGTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.88
4 3 0.07
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:4435960 original size:15 final size:15
Alignment explanation
Indices: 4435941--4435976 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
4435931 ATTATCTCTA
4435941 ATATATGTATATATT
1 ATATATGTATATATT
* *
4435956 GTATATGTTTATATT
1 ATATATGTATATATT
4435971 ATATAT
1 ATATAT
4435977 ATATTATTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (15 bp):
ATATATGTATATATT
Found at i:4436281 original size:20 final size:22
Alignment explanation
Indices: 4436242--4436281 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
4436232 ATGTTAGTAC
4436242 ATATATTTTATTATACGTATAT
1 ATATATTTTATTATACGTATAT
4436264 ATATATTTTA-TATA-GTAT
1 ATATATTTTATTATACGTAT
4436282 TATTTTCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 4 0.22
22 10 0.56
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (22 bp):
ATATATTTTATTATACGTATAT
Found at i:4440740 original size:19 final size:19
Alignment explanation
Indices: 4440716--4440832 Score: 193
Period size: 19 Copynumber: 6.2 Consensus size: 19
4440706 AATCTTTAAG
4440716 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
4440735 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
4440754 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
4440771 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
4440790 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
4440809 GATATGCAATCTTAAAGATAT
1 GATATGCAATCTT--AGATAT
4440830 GAT
1 GAT
4440833 CTTGTAATCA
Statistics
Matches: 92, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
17 16 0.17
19 67 0.73
21 9 0.10
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:4440745 original size:36 final size:34
Alignment explanation
Indices: 4440706--4440830 Score: 144
Period size: 36 Copynumber: 3.4 Consensus size: 34
4440696 ATGGAAATAT
*
4440706 AATCTTTAAGGATATGCAATCTTAGATATGATATGT
1 AATC-TTAA-GATATGCAATCTTAGATATGATATGC
4440742 AATCTT-AGATATGATACAATCTTAGATATGATATGC
1 AATCTTAAGATATG---CAATCTTAGATATGATATGC
4440778 AATCTTAGATATGATATGCAATCTTAGATATGATATGC
1 AATCTT--A-A-GATATGCAATCTTAGATATGATATGC
4440816 AATCTTAAAGATATG
1 AATCTT-AAGATATG
4440831 ATCTTGTAAT
Statistics
Matches: 79, Mismatches: 2, Indels: 17
0.81 0.02 0.17
Matches are distributed among these distances:
33 6 0.08
34 1 0.01
35 8 0.10
36 30 0.38
37 1 0.01
38 26 0.33
40 1 0.01
41 6 0.08
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (34 bp):
AATCTTAAGATATGCAATCTTAGATATGATATGC
Found at i:4440779 original size:55 final size:57
Alignment explanation
Indices: 4440716--4440832 Score: 193
Period size: 55 Copynumber: 2.1 Consensus size: 57
4440706 AATCTTTAAG
*
4440716 GATATGCAATCTTAGATATGATATGTAATCTTAGATATGATA-CAATCTT-AGATAT
1 GATATGCAATCTTAGATATGATATGCAATCTTAGATATGATAGCAATCTTAAGATAT
4440771 GATATGCAATCTTAGATATGATATGCAATCTTAGATATGATATGCAATCTTAAAGATAT
1 GATATGCAATCTTAGATATGATATGCAATCTTAGATATGATA-GCAATCTT-AAGATAT
4440830 GAT
1 GAT
4440833 CTTGTAATCA
Statistics
Matches: 57, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
55 41 0.72
57 7 0.12
59 9 0.16
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.37
Consensus pattern (57 bp):
GATATGCAATCTTAGATATGATATGCAATCTTAGATATGATAGCAATCTTAAGATAT
Found at i:4442856 original size:25 final size:24
Alignment explanation
Indices: 4442797--4442843 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
4442787 AGAACCAATC
4442797 AAATTTGAAAACATTCTTTTTGAA
1 AAATTTGAAAACATTCTTTTTGAA
*
4442821 AAATTTGAAAACGTTCTTTTTGA
1 AAATTTGAAAACATTCTTTTTGA
4442844 CTAACTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.43
Consensus pattern (24 bp):
AAATTTGAAAACATTCTTTTTGAA
Found at i:4448520 original size:2 final size:2
Alignment explanation
Indices: 4448515--4448542 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4448505 ATATTAATTA
4448515 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4448543 CTAGTTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4448666 original size:2 final size:2
Alignment explanation
Indices: 4448659--4448685 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4448649 TCCTATTTAC
4448659 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4448686 TAATACTCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4449722 original size:126 final size:126
Alignment explanation
Indices: 4449497--4449757 Score: 380
Period size: 126 Copynumber: 2.1 Consensus size: 126
4449487 GTCGACTTTA
* * ** *
4449497 TAAAACAAAGGCGAAGTTTGATGTTTAGCAATTCGAGGGTTCGTACCCTAATGTGTTGGGTTTCA
1 TAAAACAAAGGCGAAGTTTGATGTTTAGAAATTCAAGGAATCGTACCCTAATGTGCTGGGTTTCA
* *
4449562 ATCTTTCGTTTGTTTAAATAATCAAATTTCCCTTTAAAATTTTGTCC-TGTTTTCTAAACCT
66 ATCTTTCGTTTGTCTAAATAATCAAATTTCCCTTTAAAATTTCGTCCGTGTTTTCTAAA-CT
** * *
4449623 TAAAACAAAGGCGATTTTTGATGTTTAGAAATTCAAGGAATCGTGCCCTAATGTGCTGGGTTTCG
1 TAAAACAAAGGCGAAGTTTGATGTTTAGAAATTCAAGGAATCGTACCCTAATGTGCTGGGTTTCA
* *
4449688 ATCTTTCGTTTGTCTAAATAATCAGATTTCCCTTTTAAATTTCGTCCGTGTTTTCTAAACT
66 ATCTTTCGTTTGTCTAAATAATCAAATTTCCCTTTAAAATTTCGTCCGTGTTTTCTAAACT
4449749 TCAAAACAA
1 T-AAAACAA
4449758 GGAAATATTT
Statistics
Matches: 120, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
126 102 0.85
127 18 0.15
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.39
Consensus pattern (126 bp):
TAAAACAAAGGCGAAGTTTGATGTTTAGAAATTCAAGGAATCGTACCCTAATGTGCTGGGTTTCA
ATCTTTCGTTTGTCTAAATAATCAAATTTCCCTTTAAAATTTCGTCCGTGTTTTCTAAACT
Found at i:4449805 original size:126 final size:126
Alignment explanation
Indices: 4449542--4449815 Score: 340
Period size: 126 Copynumber: 2.2 Consensus size: 126
4449532 AGGGTTCGTA
* * * * *
4449542 CCCTAATGTGTTGGGTTTCAATCTTTCGTTTGTTTAAATAATCAAATTTCCCTTTAAAATTTTGT
1 CCCTAACGTGCTGGGTTTCGATCTTTCGTTTGTCTAAATAATCAAATTTCCCTTTAAAATTTCGT
** * *
4449607 CCTGTTTTCTAAACCTTAAAACAAAGGCGATTTTTGATGTTTAGAAATTCAAGGAATCGTG
66 CCTGTTTTCTAAACCTTAAAACAAAGGAAATTTTTGATGTTTAGAAATTCAAGAAATCATG
* * *
4449668 CCCTAATGTGCTGGGTTTCGATCTTTCGTTTGTCTAAATAATCAGATTTCCCTTTTAAATTTCGT
1 CCCTAACGTGCTGGGTTTCGATCTTTCGTTTGTCTAAATAATCAAATTTCCCTTTAAAATTTCGT
* **
4449733 CCGTGTTTTCTAAA-CTTCAAAAC-AAGGAAATATTTTG-TGTTTGGAAATTTTGAGAAATCATG
66 CC-TGTTTTCTAAACCTT-AAAACAAAGGAAAT-TTTTGATGTTTAGAAA-TTCAAGAAATCATG
*
4449795 CCCT-ACGTGCTAGGTTTCGAT
1 CCCTAACGTGCTGGGTTTCGAT
4449816 TTACCGTTTG
Statistics
Matches: 129, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
126 94 0.73
127 35 0.27
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (126 bp):
CCCTAACGTGCTGGGTTTCGATCTTTCGTTTGTCTAAATAATCAAATTTCCCTTTAAAATTTCGT
CCTGTTTTCTAAACCTTAAAACAAAGGAAATTTTTGATGTTTAGAAATTCAAGAAATCATG
Found at i:4451630 original size:26 final size:26
Alignment explanation
Indices: 4451601--4451708 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
4451591 TGGTACAAAT
4451601 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
4451627 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
4451653 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
4451679 TGATAATGGTTTAGGTAAATGTTCTA
1 TGATAATGGGTTAGGTAAATGTTCCA
4451705 TGAT
1 TGAT
4451709 GGGCATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:4454465 original size:19 final size:19
Alignment explanation
Indices: 4454441--4454486 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
4454431 CTCTCTTTCT
4454441 TTTGCATT-CATTCCATACA
1 TTTGCATTGCATTCCAT-CA
*
4454460 TTTGCATTGCATTGCATCA
1 TTTGCATTGCATTCCATCA
*
4454479 TTTACATT
1 TTTGCATT
4454487 AAACTTTCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.46
Consensus pattern (19 bp):
TTTGCATTGCATTCCATCA
Found at i:4456698 original size:16 final size:16
Alignment explanation
Indices: 4456674--4456712 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
4456664 TAGCAAAGGC
4456674 AAAAAAAAACGA-AAAG
1 AAAAAAAAA-GAGAAAG
*
4456690 AAAAGAAAAGAGAAAG
1 AAAAAAAAAGAGAAAG
4456706 AAAAAAA
1 AAAAAAA
4456713 CAAAAACAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 2 0.10
16 18 0.90
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGAGAAAG
Found at i:4457690 original size:52 final size:52
Alignment explanation
Indices: 4457572--4457722 Score: 202
Period size: 48 Copynumber: 3.0 Consensus size: 52
4457562 GCTCCCAACA
*
4457572 AATTTCCTTCTTATTACATTGCTATCTTTGATTAAC---TT-ATTTCGAGTT
1 AATTTCCTTCTTATTGCATTGCTATCTTTGATTAACTTATTCATTTCGAGTT
* * *
4457620 AATTTCCTTCTTATTGCATTGTTATCTTTCATTAACTTATTCATTTTGAGTT
1 AATTTCCTTCTTATTGCATTGCTATCTTTGATTAACTTATTCATTTCGAGTT
* * *
4457672 AATTTCTTTCTTATTGCATTTGCAATCTTTGATTAATTTATTCATTTCGAG
1 AATTTCCTTCTTATTGCA-TTGCTATCTTTGATTAACTTATTCATTTCGAG
4457723 CTATACTCCC
Statistics
Matches: 88, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
48 33 0.38
51 2 0.02
52 26 0.30
53 27 0.31
ACGTcount: A:0.23, C:0.15, G:0.09, T:0.54
Consensus pattern (52 bp):
AATTTCCTTCTTATTGCATTGCTATCTTTGATTAACTTATTCATTTCGAGTT
Found at i:4457693 original size:26 final size:26
Alignment explanation
Indices: 4457610--4457693 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
4457600 TGATTAACTT
*
4457610 ATTTCGAGTTAATTTCCTTCTTATTGC
1 ATTT-GAGTTAATTTCTTTCTTATTGC
* *
4457637 A-TT--GTTATCTTTCATTAACTTATT-C
1 ATTTGAGTTA-ATTTC-TT-TCTTATTGC
4457662 ATTTTGAGTTAATTTCTTTCTTATTGC
1 A-TTTGAGTTAATTTCTTTCTTATTGC
4457689 ATTTG
1 ATTTG
4457694 CAATCTTTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 17
0.67 0.08 0.26
Matches are distributed among these distances:
23 4 0.09
24 4 0.09
25 3 0.07
26 18 0.41
27 7 0.16
28 4 0.09
29 4 0.09
ACGTcount: A:0.20, C:0.14, G:0.10, T:0.56
Consensus pattern (26 bp):
ATTTGAGTTAATTTCTTTCTTATTGC
Found at i:4458545 original size:64 final size:64
Alignment explanation
Indices: 4458471--4458595 Score: 205
Period size: 64 Copynumber: 2.0 Consensus size: 64
4458461 TTCATAACAC
* * *
4458471 ATCTAGTTAGGAGCATTTGATTTATTTTGATCATAGCATCCTAGTTATTTGACATAAGCATCAT
1 ATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGCATCAT
* *
4458535 ATCTAGTTAGGAGCATTTGATTCATTTCGATCATGGCATCCTAATTATTTGGCATAAGCAT
1 ATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGCAT
4458596 GGATACATGA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (64 bp):
ATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGCATCAT
Found at i:4458821 original size:45 final size:44
Alignment explanation
Indices: 4458770--4458954 Score: 115
Period size: 45 Copynumber: 4.2 Consensus size: 44
4458760 TCCATAAGAA
* *
4458770 GTAGTGGAGTAGGTTGAAGATTGTAGATCTTGTCTCCTTGAAGTT
1 GTAGTGGAGCAGATTGAAGATTG-AGATCTTGTCTCCTTGAAGTT
* * * * * *
4458815 GTAGTGGAACAGATCGAAAATGGCGAACCTTGTCT-CTCTGAAGTT
1 GTAGTGGAGCAGATTGAAGATTGAG-ATCTTGTCTCCT-TGAAGTT
* ** ** * * *
4458860 GTAGTGGAGCAGATTTAAG-CCGCCATCCTATCTCCTT-AAGTA
1 GTAGTGGAGCAGATTGAAGATTGAGATCTTGTCTCCTTGAAGTT
* * ** *
4458902 GTAGTGAAGTAGGCTGAAGATTGCAGATCTTGTCTCCCTGAAGTT
1 GTAGTGGAGCAGATTGAAGATTG-AGATCTTGTCTCCTTGAAGTT
*
4458947 GCAGTGGA
1 GTAGTGGA
4458955 ACTGATCGAA
Statistics
Matches: 100, Mismatches: 34, Indels: 12
0.68 0.23 0.08
Matches are distributed among these distances:
42 18 0.18
43 8 0.08
44 17 0.17
45 57 0.57
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.30
Consensus pattern (44 bp):
GTAGTGGAGCAGATTGAAGATTGAGATCTTGTCTCCTTGAAGTT
Found at i:4459056 original size:131 final size:129
Alignment explanation
Indices: 4458662--4459097 Score: 550
Period size: 131 Copynumber: 3.3 Consensus size: 129
4458652 GGTGAATTTA
* * * * *
4458662 CAGATCTCGTCTCCCTGAAGTTGCAATGGAATAGATCGAAGACAGCGAATCTCGTCTCTCTGAAG
1 CAGATCTTGTCTCCCTGAAGTTGCAGTGGAACAGATCGAAGACGGCGAATCTTGTCTCTCTGAAG
* ** * *
4458727 TTGCAGTGGAGCAAATTTAAG-TTCCATCCTATCTCCATAAGAAGTAGTGGAGTAGGTTGAAGAT
66 -T--AGTGGAGCAGATTTAAGCCACCATCCTATCTCCATAAGTAGTAGTGGAGTAGGCTGAAGAT
4458791 TG
128 TG
* * * * * *
4458793 TAGATCTTGTCTCCTTGAAGTTGTAGTGGAACAGATCGAAAATGGCGAACCTTGTCTCTCTGAAG
1 CAGATCTTGTCTCCCTGAAGTTGCAGTGGAACAGATCGAAGACGGCGAATCTTGTCTCTCTGAA-
* * *
4458858 TTGTAGTGGAGCAGATTTAAGCCGCCATCCTATCTCCTTAAGTAGTAGTGAAGTAGGCTGAAGAT
65 --GTAGTGGAGCAGATTTAAGCCACCATCCTATCTCCATAAGTAGTAGTGGAGTAGGCTGAAGAT
4458923 TG
128 TG
* *
4458925 CAGATCTTGTCTCCCTGAAGTTGCAGTGGAACTGATCGAAGACGGCGAATCTTGTCTCCCTGACC
1 CAGATCTTGTCTCCCTGAAGTTGCAGTGGAACAGATCGAAGACGGCGAATCTTGTCTCTCTGA--
* * * *
4458990 AGTAGTGGAACGGATTTAAGCCACCATTCTATCTCCCTAAGTAGTAGTGGAGTAGGCTGAAGATT
64 AGTAGTGGAGCAGATTTAAGCCACCATCCTATCTCCATAAGTAGTAGTGGAGTAGGCTGAAGATT
4459055 G
129 G
* *
4459056 CAGATCTTGTCTCTCTGAAGTTGCAGTGGAACAGATCAAAGA
1 CAGATCTTGTCTCCCTGAAGTTGCAGTGGAACAGATCGAAGA
4459098 TGGTGAGCCT
Statistics
Matches: 264, Mismatches: 35, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
131 167 0.63
132 94 0.36
133 1 0.00
134 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.28
Consensus pattern (129 bp):
CAGATCTTGTCTCCCTGAAGTTGCAGTGGAACAGATCGAAGACGGCGAATCTTGTCTCTCTGAAG
TAGTGGAGCAGATTTAAGCCACCATCCTATCTCCATAAGTAGTAGTGGAGTAGGCTGAAGATTG
Done.