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 194 of 292
Found at i:57920720 original size:80 final size:80
Alignment explanation
Indices: 57920587--57920754 Score: 246
Period size: 80 Copynumber: 2.1 Consensus size: 80
57920577 CAATTGAATG
* * * *
57920587 ATATCCGGGTTACGACCCGAAGGCAATTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTCACTATATCCGGGCTAAGACCCGAAGGCA
*
57920652 TTCGTGCAAGTTGTT
66 TTCGTGCAAGTGGTT
* * *
57920667 ATATCCGGGCTAATACCCGAAGGCATTTGTGCGAGTCATTATATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTCACTATATCCGGGCTAAGACCCGAAGGCA
**
57920732 TTCGTGCGTGTGGTT
66 TTCGTGCAAGTGGTT
57920747 ATATCCGG
1 ATATCCGG
57920755 TTGTATTCCA
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
80 78 1.00
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.26
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTCACTATATCCGGGCTAAGACCCGAAGGCA
TTCGTGCAAGTGGTT
Found at i:57924563 original size:16 final size:16
Alignment explanation
Indices: 57924539--57924571 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
57924529 TTTTATATAT
*
57924539 TAAATTATTATATTAA
1 TAAAATATTATATTAA
57924555 TAAAATATTATATTAA
1 TAAAATATTATATTAA
57924571 T
1 T
57924572 TAGATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAAAATATTATATTAA
Found at i:57925299 original size:44 final size:44
Alignment explanation
Indices: 57925249--57925340 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 44
57925239 TGTTTAGGGA
* *
57925249 TACTTCGACCTT-GAGTCGATGAGGCA-CTATGAGTGTCGTACTGT
1 TACTTCGA-CTTCAAGTCGATAAGGCACCT-TGAGTGTCGTACTGT
*
57925293 TACTTCGACTTCAAGTCGATAAGGCACCTTGTGTGTCGTACTGT
1 TACTTCGACTTCAAGTCGATAAGGCACCTTGAGTGTCGTACTGT
57925337 TACT
1 TACT
57925341 ATTACTTTGG
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 3 0.07
44 38 0.88
45 2 0.05
ACGTcount: A:0.21, C:0.22, G:0.24, T:0.34
Consensus pattern (44 bp):
TACTTCGACTTCAAGTCGATAAGGCACCTTGAGTGTCGTACTGT
Found at i:57928659 original size:22 final size:22
Alignment explanation
Indices: 57928620--57928661 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
57928610 ATATTGTGTA
*
57928620 ACATATCATAACACATCTCATG
1 ACATATCATAACAAATCTCATG
* *
57928642 ACATATCTTAGCAAATCTCA
1 ACATATCATAACAAATCTCA
57928662 AATCATATCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.26, G:0.05, T:0.29
Consensus pattern (22 bp):
ACATATCATAACAAATCTCATG
Found at i:57928710 original size:27 final size:27
Alignment explanation
Indices: 57928663--57928730 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
57928653 CAAATCTCAA
*
57928663 ATCATATCATATCATAGCATAGTATAAT
1 ATCATATCATATCATAACATA-TATAAT
*
57928691 A-CATATCATAT-ATTAACATATATTAT
1 ATCATATCATATCA-TAACATATATAAT
*
57928717 ATCATATCCTATCA
1 ATCATATCATATCA
57928731 CTGTTCGCTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 7 0.21
27 25 0.74
28 2 0.06
ACGTcount: A:0.43, C:0.16, G:0.03, T:0.38
Consensus pattern (27 bp):
ATCATATCATATCATAACATATATAAT
Found at i:57929929 original size:206 final size:205
Alignment explanation
Indices: 57929575--57929975 Score: 669
Period size: 206 Copynumber: 2.0 Consensus size: 205
57929565 TGGCATCCCG
*
57929575 AGGTACTTTTGATAGGGCATTGGTTGGGGATGGCTTTGGTGGCTAACGTGGTAGTTTGGGGGCTA
1 AGGTACTTTTGATAGGGCATTGGTTGGGGATAGCTTTGGTGGCTAACGTGGTAGTTTGGGGGCTA
* * * * *
57929640 TTTTGGGGTGGTTTCATGACCTTCCCGACTGCCACACGGGCGTGTGCTGAGGCACACGGCTGTGT
66 TTTTGGGGTGGTTTCATGACCTCCCCGACTACCACACGGGCATGTGCTAAGGCACACGACTGTGT
*
57929705 GGATTTGGGGATTAGGGTTT-TGAGCCAAATTTAGTGCAACACGACCGTGTGACCGATTGAGGGA
131 GGATTTGGGGATTAGGGTTTCAG-GCCAAATTTAGTGCAACACGACCGTGTGACCGATTG-GGGA
57929769 TTAGGCTTCCTA
194 TTAGGCTTCCTA
*
57929781 AGGTACTTTTGATAGGGCATTGGTTGGGGATAGCTTTGGTGGCTAACGTGGTGGTTTGGGGGCTA
1 AGGTACTTTTGATAGGGCATTGGTTGGGGATAGCTTTGGTGGCTAACGTGGTAGTTTGGGGGCTA
* *
57929846 TTTTGGGGTGGTTTCGTGACCTCCCCTACTACCACACGGGCATGTGCTAAGGCACACGACTGTGT
66 TTTTGGGGTGGTTTCATGACCTCCCCGACTACCACACGGGCATGTGCTAAGGCACACGACTGTGT
* *
57929911 GGATTTGGGGATTAGGGTTTCAGGCCAAATTTGGTGCAATACGACCGTGTGACCGATTGGGGATT
131 GGATTTGGGGATTAGGGTTTCAGGCCAAATTTAGTGCAACACGACCGTGTGACCGATTGGGGATT
57929976 TCGTCGTTTC
Statistics
Matches: 182, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
205 6 0.03
206 175 0.96
207 1 0.01
ACGTcount: A:0.18, C:0.17, G:0.35, T:0.30
Consensus pattern (205 bp):
AGGTACTTTTGATAGGGCATTGGTTGGGGATAGCTTTGGTGGCTAACGTGGTAGTTTGGGGGCTA
TTTTGGGGTGGTTTCATGACCTCCCCGACTACCACACGGGCATGTGCTAAGGCACACGACTGTGT
GGATTTGGGGATTAGGGTTTCAGGCCAAATTTAGTGCAACACGACCGTGTGACCGATTGGGGATT
AGGCTTCCTA
Found at i:57932545 original size:16 final size:16
Alignment explanation
Indices: 57932524--57932557 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
57932514 TATTAACAAA
*
57932524 GTTAGTATCAGCAGTG
1 GTTAGTACCAGCAGTG
57932540 GTTAGTACCAGCAGTG
1 GTTAGTACCAGCAGTG
57932556 GT
1 GT
57932558 ACGAGCATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.15, G:0.32, T:0.29
Consensus pattern (16 bp):
GTTAGTACCAGCAGTG
Found at i:57933156 original size:16 final size:15
Alignment explanation
Indices: 57933138--57933211 Score: 71
Period size: 17 Copynumber: 4.8 Consensus size: 15
57933128 TGTCGTTTTA
*
57933138 ATTATTCTTTTTATT
1 ATTATTATTTTTATT
57933153 AATTATTTATTTTTATT
1 -ATTA-TTATTTTTATT
*
57933170 GTTATAATATTTTTATT
1 ATTAT--TATTTTTATT
*
57933187 ATTCTTATTTTTA-T
1 ATTATTATTTTTATT
57933201 -TTATTATTTTT
1 ATTATTATTTTT
57933212 CTTTTCTGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
13 10 0.20
14 1 0.02
15 9 0.18
16 7 0.14
17 23 0.46
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.72
Consensus pattern (15 bp):
ATTATTATTTTTATT
Found at i:57936434 original size:8 final size:8
Alignment explanation
Indices: 57936422--57936461 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
57936412 CAAGAGCACC
*
57936422 AAAAGAAC
1 AAAAGAAA
57936430 AAAAGAAA
1 AAAAGAAA
57936438 ACAAAGAAA
1 A-AAAGAAA
*
57936447 TAAAGAAA
1 AAAAGAAA
57936455 AAAAGAA
1 AAAAGAA
57936462 TAGGAAGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
8 21 0.75
9 7 0.25
ACGTcount: A:0.80, C:0.05, G:0.12, T:0.03
Consensus pattern (8 bp):
AAAAGAAA
Found at i:57936445 original size:17 final size:17
Alignment explanation
Indices: 57936431--57936476 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
57936421 CAAAAGAACA
*
57936431 AAAGAAAACAAAGAAAT
1 AAAGAAAACAAAGAAAG
57936448 AAAGAAAA-AAAGAATAG
1 AAAGAAAACAAAGAA-AG
*
57936465 GAAGAAAACAAA
1 AAAGAAAACAAA
57936477 ACAAAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 6 0.24
17 16 0.64
18 3 0.12
ACGTcount: A:0.76, C:0.04, G:0.15, T:0.04
Consensus pattern (17 bp):
AAAGAAAACAAAGAAAG
Found at i:57938356 original size:17 final size:18
Alignment explanation
Indices: 57938314--57938356 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
57938304 TAAATAAATC
57938314 TAAA-TAAAACTCTTAAG
1 TAAACTAAAACTCTTAAG
* *
57938331 TATACTAAAACTC-TAAT
1 TAAACTAAAACTCTTAAG
57938348 TAAACTAAA
1 TAAACTAAA
57938357 CAAGAAGAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.30
Consensus pattern (18 bp):
TAAACTAAAACTCTTAAG
Found at i:57939106 original size:13 final size:14
Alignment explanation
Indices: 57939083--57939111 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
57939073 TAACCATAAA
57939083 TTTAGCCTTTTATG
1 TTTAGCCTTTTATG
57939097 TTTA-CCTTTTATG
1 TTTAGCCTTTTATG
57939110 TT
1 TT
57939112 ATATTGGCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.14, C:0.14, G:0.10, T:0.62
Consensus pattern (14 bp):
TTTAGCCTTTTATG
Found at i:57940478 original size:30 final size:29
Alignment explanation
Indices: 57940444--57940513 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 29
57940434 AAAAAACAAA
*
57940444 TTTTAACATCCTTGTAAT-TTAAATAAAAAC
1 TTTTAA-ATACTT-TAATATTAAATAAAAAC
*
57940474 TTTTAAATAGTTTAATAACTTAAATAAAAAC
1 TTTTAAATACTTTAAT-A-TTAAATAAAAAC
57940505 TTTTAAATA
1 TTTTAAATA
57940514 ATTGACCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 4 0.11
29 4 0.11
30 6 0.17
31 21 0.60
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (29 bp):
TTTTAAATACTTTAATATTAAATAAAAAC
Found at i:57952069 original size:138 final size:138
Alignment explanation
Indices: 57951749--57952162 Score: 649
Period size: 135 Copynumber: 3.0 Consensus size: 138
57951739 AGTGGGAGGC
57951749 TCTGGATCATATTGTCTATATCCAATGGTATTAGTTTCGTTATTATTAACAGCATTCA-CTGGCC
1 TCTGGATCATATTGTCTATATCCAATGGTATTAGTTTCGTTATTATTAACAGCATTCACCT-GCC
57951813 TCGAGTTTGAAGCAGACAAATCAGATCCTCCTCCGTCTTTCTTGGCCCAATTCCTCGTCTTTTCC
65 TCGAGTTTGAAGCAGACAAATCAGATCCTCCTCCGTCTTTCTTGGCCCAATTCCTCGTCTTTTCC
*
57951878 GGTTTTTCT
130 AGTTTTTCT
* * * *
57951887 TCTGGATCATATTGTCTATTTCCGACGGTATTAGTTTCATTATTATTAACAGCATTCACCTGCCT
1 TCTGGATCATATTGTCTATATCCAATGGTATTAGTTTCGTTATTATTAACAGCATTCACCTGCCT
* * *
57951952 CAAGTTTGAAGCAGAAAAATCGGATCCTCCAT-C-T-TTT-TTGGCCCAATTCCTCGTCTTTTCC
66 CGAGTTTGAAGCAGACAAATCAGATCCTCC-TCCGTCTTTCTTGGCCCAATTCCTCGTCTTTTCC
*
57952013 TGTTTTTCT
130 AGTTTTTCT
*
57952022 TCTGGATCATATTGTCTATGTCCAATGGTATTAGTTTCGTTATTATTAACAGCATTCACCTGCCT
1 TCTGGATCATATTGTCTATATCCAATGGTATTAGTTTCGTTATTATTAACAGCATTCACCTGCCT
* * * *
57952087 CGAGTTTGAAGCATACGAATCAGATCCTCCTCCGTCTTTCTTTGCCCAATTCCTTGTCTTTTCCA
66 CGAGTTTGAAGCAGACAAATCAGATCCTCCTCCGTCTTTCTTGGCCCAATTCCTCGTCTTTTCCA
57952152 GTTTTTCT
131 GTTTTTCT
57952160 TCT
1 TCT
57952163 CTAGTTGCTT
Statistics
Matches: 250, Mismatches: 20, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
134 1 0.00
135 119 0.48
136 4 0.02
137 4 0.02
138 119 0.48
139 3 0.01
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (138 bp):
TCTGGATCATATTGTCTATATCCAATGGTATTAGTTTCGTTATTATTAACAGCATTCACCTGCCT
CGAGTTTGAAGCAGACAAATCAGATCCTCCTCCGTCTTTCTTGGCCCAATTCCTCGTCTTTTCCA
GTTTTTCT
Found at i:57956368 original size:73 final size:74
Alignment explanation
Indices: 57956249--57956453 Score: 243
Period size: 73 Copynumber: 2.7 Consensus size: 74
57956239 GTCATGAGAG
* * * *
57956249 TGTTCACCAAATAAGTTCATAAAAAATGACAATTTTAAATAAATTAAAAG-TATACATTAATCAA
1 TGTTCACCAAATAAGTTTAAAAAAAATGACAATTTAAAATAAATTAAAAGATATACATTAACCAA
57956313 ATTCAATTA
66 ATTCAATTA
* *
57956322 TGTTCACCGAATAAGTTTAAAAAAAATAACAATTTAAAATAAATTAAAAGCCATTAAATATATAC
1 TGTTCACCAAATAAGTTTAAAAAAAATGACAATTTAAAATAAATTAAAAG---------ATATAC
57956387 ATTAACCAAATTCAATTA
57 ATTAACCAAATTCAATTA
* *
57956405 TGTTCACCAAATAAG-TTCATAAAAATGACAATTTAAAATAAATTAAAAG
1 TGTTCACCAAATAAGTTTAAAAAAAATGACAATTTAAAATAAATTAAAAG
57956454 CAATTAAATA
Statistics
Matches: 112, Mismatches: 10, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
73 45 0.40
82 31 0.28
83 36 0.32
ACGTcount: A:0.52, C:0.11, G:0.06, T:0.31
Consensus pattern (74 bp):
TGTTCACCAAATAAGTTTAAAAAAAATGACAATTTAAAATAAATTAAAAGATATACATTAACCAA
ATTCAATTA
Found at i:57956450 original size:82 final size:83
Alignment explanation
Indices: 57956290--57956483 Score: 302
Period size: 82 Copynumber: 2.3 Consensus size: 83
57956280 ATTTTAAATA
* *
57956290 AATTAAA-AGTATACATTAATCAAATTCAATTATGTTCACCGAATAAGTTTAAAAAAAATAACAA
1 AATTAAATA-TATACATTAACCAAATTCAATTATGTTCACCAAATAAGTTTAAAAAAAATAACAA
57956354 TTTAAAATAAATTAAAAGC
65 TTTAAAATAAATTAAAAGC
* * * *
57956373 CATTAAATATATACATTAACCAAATTCAATTATGTTCACCAAATAAG-TTCATAAAAATGACAAT
1 AATTAAATATATACATTAACCAAATTCAATTATGTTCACCAAATAAGTTTAAAAAAAATAACAAT
57956437 TTAAAATAAATTAAAAGC
66 TTAAAATAAATTAAAAGC
*
57956455 AATTAAATATATACATTAACCGAATTCAA
1 AATTAAATATATACATTAACCAAATTCAA
57956484 ATTGCCGCAT
Statistics
Matches: 102, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
82 59 0.58
83 42 0.41
84 1 0.01
ACGTcount: A:0.53, C:0.12, G:0.05, T:0.30
Consensus pattern (83 bp):
AATTAAATATATACATTAACCAAATTCAATTATGTTCACCAAATAAGTTTAAAAAAAATAACAAT
TTAAAATAAATTAAAAGC
Found at i:57959222 original size:20 final size:20
Alignment explanation
Indices: 57959197--57959250 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
57959187 AAGTTAAGTA
*
57959197 TTTATATTAAATTAATATAT
1 TTTATATTAAATTAAGATAT
*
57959217 TTTATAATAAATTTAAGATAT
1 TTTATATTAAA-TTAAGATAT
57959238 TTTATATTTAAAT
1 TTTATA-TTAAAT
57959251 ATATTCTAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 10 0.34
21 15 0.52
22 4 0.14
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TTTATATTAAATTAAGATAT
Found at i:57959237 original size:21 final size:20
Alignment explanation
Indices: 57959184--57959243 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
57959174 TTGTAGATTA
*
57959184 AATAAGTTAAG-TA-TTTAT
1 AATAAATTAAGATATTTTAT
* *
57959202 ATTAAATTAATATATTTTAT
1 AATAAATTAAGATATTTTAT
57959222 AATAAATTTAAGATATTTTAT
1 AATAAA-TTAAGATATTTTAT
57959243 A
1 A
57959244 TTTAAATATA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
18 8 0.24
19 2 0.06
20 10 0.29
21 14 0.41
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (20 bp):
AATAAATTAAGATATTTTAT
Found at i:57959296 original size:18 final size:20
Alignment explanation
Indices: 57959273--57959311 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
57959263 ATTAATAGTT
*
57959273 TATA-TTATA-ATTTTTTTA
1 TATATTTATATATTATTTTA
57959291 TATATTTATATATTATTTTA
1 TATATTTATATATTATTTTA
57959311 T
1 T
57959312 TTTTATTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 5 0.28
20 9 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TATATTTATATATTATTTTA
Found at i:57962490 original size:43 final size:43
Alignment explanation
Indices: 57962409--57962490 Score: 98
Period size: 43 Copynumber: 1.9 Consensus size: 43
57962399 AAGTCGTACA
**
57962409 ATGCCAACGTCCCAGACGTGGTCTTACATGTAGTCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGTAAACACATATCG
57962452 ATGCC-ACAGTCCCAGACAG-GGTCTTAC-TCGTAAACACAT
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACAT-GTAAACACAT
57962491 CTCGGAATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
42 3 0.09
43 30 0.88
44 1 0.03
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACATGTAAACACATATCG
Found at i:57962550 original size:30 final size:30
Alignment explanation
Indices: 57962514--57962573 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
57962504 ATCGATGCCA
57962514 TGGTCTTACTCGCACACATATATCAGAATC
1 TGGTCTTACTCGCACACATATATCAGAATC
57962544 TGGTCTTACTCGCACACATATATCAGAATC
1 TGGTCTTACTCGCACACATATATCAGAATC
57962574 CTATGTCATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (30 bp):
TGGTCTTACTCGCACACATATATCAGAATC
Found at i:57965360 original size:40 final size:40
Alignment explanation
Indices: 57965305--57965522 Score: 300
Period size: 40 Copynumber: 5.5 Consensus size: 40
57965295 CGGATGATAA
* *
57965305 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
57965345 CCGGGCTAAGTCCCGAAGGCCTTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
* *
57965385 TCGGGCTAAGTCCCGAAGGCCTTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
57965425 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
57965465 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
57965505 CC-GGCTAAATCCTGAAGG
1 CCGGGCTAAGTCCCGAAGG
57965523 TACTTGGTTT
Statistics
Matches: 165, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
39 16 0.10
40 148 0.90
41 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:57965551 original size:38 final size:38
Alignment explanation
Indices: 57965508--57965583 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
57965498 GCTATATCCG
57965508 GCTAAATCCTGAAGGTACTTGGTTTGGGAATGAGCGAT
1 GCTAAATCCTGAAGGTACTTGGTTTGGGAATGAGCGAT
57965546 GCTAAATCCTGAAGGTACTTGGTTTGGGAATGAGCGAT
1 GCTAAATCCTGAAGGTACTTGGTTTGGGAATGAGCGAT
57965584 CTTGCTGTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.26, C:0.13, G:0.32, T:0.29
Consensus pattern (38 bp):
GCTAAATCCTGAAGGTACTTGGTTTGGGAATGAGCGAT
Found at i:57974702 original size:29 final size:29
Alignment explanation
Indices: 57974669--57974771 Score: 143
Period size: 29 Copynumber: 3.6 Consensus size: 29
57974659 CCTCCGAACT
** * * *
57974669 CGCACACCCAGTGCCGTATTTTTCCAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
* *
57974698 TGCACACTTAGTGCCAAATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
57974727 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
57974756 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
57974772 ATCTCGTCAC
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 65 1.00
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.26
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:57980576 original size:29 final size:29
Alignment explanation
Indices: 57980543--57980645 Score: 143
Period size: 29 Copynumber: 3.6 Consensus size: 29
57980533 CCTCCGAACT
** * * *
57980543 CGCACACCCAGTGCCGTATTTTTCCAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
* *
57980572 TGCACACTTAGTGCCAAATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
57980601 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
57980630 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
57980646 ATCTCGTCAC
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 65 1.00
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.26
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:57988500 original size:29 final size:29
Alignment explanation
Indices: 57988458--57988559 Score: 143
Period size: 29 Copynumber: 3.6 Consensus size: 29
57988448 CCTCCGAACT
* * * *
57988458 CGCACAC-CAGTGCCGTATTTTTCCAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
* *
57988486 TGCACACTTAGTGCCAAATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
57988515 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
57988544 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
57988560 ATCTCGTCAC
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
28 6 0.09
29 59 0.91
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.26
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:57994860 original size:40 final size:40
Alignment explanation
Indices: 57994805--57994884 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
57994795 ACAAGTAGTT
57994805 AACTAGAATTCTTGGTTGCATGTTGGTTGCTTAAGAATCA
1 AACTAGAATTCTTGGTTGCATGTTGGTTGCTTAAGAATCA
57994845 AACTAGAATTCTTGGTTGCATGTTGGTTGCTTAAGAATCA
1 AACTAGAATTCTTGGTTGCATGTTGGTTGCTTAAGAATCA
57994885 CTTAGTTCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.38
Consensus pattern (40 bp):
AACTAGAATTCTTGGTTGCATGTTGGTTGCTTAAGAATCA
Found at i:58001525 original size:17 final size:17
Alignment explanation
Indices: 58001503--58001538 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
58001493 TCTCAAGCAA
58001503 CTCTTTTAATCAGGTTC
1 CTCTTTTAATCAGGTTC
58001520 CTCTTTTAATCAGGTTC
1 CTCTTTTAATCAGGTTC
58001537 CT
1 CT
58001539 TTGTTTGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.25, G:0.11, T:0.47
Consensus pattern (17 bp):
CTCTTTTAATCAGGTTC
Found at i:58001675 original size:68 final size:69
Alignment explanation
Indices: 58001540--58001678 Score: 244
Period size: 68 Copynumber: 2.0 Consensus size: 69
58001530 CAGGTTCCTT
* *
58001540 TGTTTGTTTCATGCTTCTTCTCGTGCCTTTTTTTTTTTTTTGTAATTTTTTATGAGTTTTAATAT
1 TGTTTGTTTCATGCTTCTTCTCGTGCC-TCTTTTCTTTTTTGTAATTTTTTATGAGTTTTAATAT
58001605 TTATG
65 TTATG
58001610 TGTTTGTTTCATGCTTCTTCTCGTGCC-CTTTTCTTTTTTGTAATTTTTTATGAGTTTTAATATT
1 TGTTTGTTTCATGCTTCTTCTCGTGCCTCTTTTCTTTTTTGTAATTTTTTATGAGTTTTAATATT
58001674 TATG
66 TATG
58001678 T
1 T
58001679 TCCGTTGCTG
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
68 40 0.60
70 27 0.40
ACGTcount: A:0.13, C:0.12, G:0.13, T:0.63
Consensus pattern (69 bp):
TGTTTGTTTCATGCTTCTTCTCGTGCCTCTTTTCTTTTTTGTAATTTTTTATGAGTTTTAATATT
TATG
Found at i:58007711 original size:19 final size:20
Alignment explanation
Indices: 58007667--58007705 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
58007657 TATTTAAGTC
58007667 TAAAAATAATTAAAATATTA
1 TAAAAATAATTAAAATATTA
58007687 TAAAAA-AATTAAAAT-TTA
1 TAAAAATAATTAAAATATTA
58007705 T
1 T
58007706 GGAAAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.21
19 9 0.47
20 6 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAAAATAATTAAAATATTA
Found at i:58007897 original size:22 final size:21
Alignment explanation
Indices: 58007853--58007934 Score: 69
Period size: 21 Copynumber: 3.8 Consensus size: 21
58007843 AAACCATTAA
*
58007853 ATATTATAAAATATTATTAAG
1 ATATTATAAAATATTAATAAG
*
58007874 ATCTTATGAAAATATTAA-ATAG
1 ATATTAT-AAAATATTAATA-AG
* * *
58007896 ATATTATAAAAAATTTAGAAG
1 ATATTATAAAATATTAATAAG
58007917 AT-TATATAAAATAATTAA
1 ATAT-TATAAAAT-ATTAA
58007935 AATTATAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
20 1 0.02
21 26 0.53
22 22 0.45
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.38
Consensus pattern (21 bp):
ATATTATAAAATATTAATAAG
Found at i:58007918 original size:43 final size:43
Alignment explanation
Indices: 58007853--58007935 Score: 100
Period size: 43 Copynumber: 1.9 Consensus size: 43
58007843 AAACCATTAA
* *
58007853 ATATTATAAAATATTATTAAGATCT-TATGAAAAT-ATTAAATAG
1 ATATTATAAAAAATTATGAAGAT-TATAT-AAAATAATTAAATAG
58007896 ATATTATAAAAAATT-TAGAAGATTATATAAAATAATTAAA
1 ATATTATAAAAAATTAT-GAAGATTATATAAAATAATTAAA
58007936 ATTATAAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
42 7 0.20
43 28 0.80
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.37
Consensus pattern (43 bp):
ATATTATAAAAAATTATGAAGATTATATAAAATAATTAAATAG
Found at i:58008211 original size:10 final size:11
Alignment explanation
Indices: 58008182--58008214 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
58008172 TAGAACTACT
58008182 AGAATATTATAA
1 AGAA-ATTATAA
58008194 AGAAATTATAA
1 AGAAATTATAA
58008205 A-AAATTATAA
1 AGAAATTATAA
58008215 GTTATTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 9 0.43
11 8 0.38
12 4 0.19
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (11 bp):
AGAAATTATAA
Found at i:58009062 original size:40 final size:40
Alignment explanation
Indices: 58009018--58009100 Score: 157
Period size: 40 Copynumber: 2.1 Consensus size: 40
58009008 GATACTTAAA
*
58009018 GTATATTTTTTTCTCAAGTTGATATTTATATGATTTTTTG
1 GTATATTTTTTTCTCAAATTGATATTTATATGATTTTTTG
58009058 GTATATTTTTTTCTCAAATTGATATTTATATGATTTTTTG
1 GTATATTTTTTTCTCAAATTGATATTTATATGATTTTTTG
58009098 GTA
1 GTA
58009101 ACAAGTGATA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.24, C:0.05, G:0.12, T:0.59
Consensus pattern (40 bp):
GTATATTTTTTTCTCAAATTGATATTTATATGATTTTTTG
Found at i:58012056 original size:20 final size:19
Alignment explanation
Indices: 58012040--58012081 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
58012030 TAAAAAAGGC
58012040 AAAAAAA-AAAAAAAAAAG
1 AAAAAAAGAAAAAAAAAAG
*
58012058 AAAAAAAGAAAAGAAAGAAG
1 AAAAAAAGAAAA-AAAAAAG
58012078 AAAA
1 AAAA
58012082 CTTTAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
19 4 0.19
20 10 0.48
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (19 bp):
AAAAAAAGAAAAAAAAAAG
Found at i:58012061 original size:17 final size:17
Alignment explanation
Indices: 58012041--58012081 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
58012031 AAAAAAGGCA
58012041 AAAAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAAAG
* *
58012058 AAAAAAAGAAAAGAAAG
1 AAAAAAAAAAAAAAAAG
58012075 AAGAAAA
1 AA-AAAA
58012082 CTTTAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAAAAAG
Found at i:58012070 original size:13 final size:13
Alignment explanation
Indices: 58012040--58012073 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
58012030 TAAAAAAGGC
58012040 AAAAA-AAAAAAA
1 AAAAAGAAAAAAA
58012052 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
*
58012065 GAAAAGAAA
1 AAAAAGAAA
58012074 GAAGAAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAA
Found at i:58012074 original size:9 final size:8
Alignment explanation
Indices: 58012042--58012081 Score: 53
Period size: 8 Copynumber: 4.8 Consensus size: 8
58012032 AAAAAGGCAA
*
58012042 AAAAAAAA
1 AAAAAAAG
58012050 AAAAAAAG
1 AAAAAAAG
58012058 AAAAAAAG
1 AAAAAAAG
58012066 AAAAGAAAG
1 AAAA-AAAG
58012075 AAGAAAA
1 AA-AAAA
58012082 CTTTAAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 19 0.66
9 8 0.28
10 2 0.07
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:58015913 original size:22 final size:22
Alignment explanation
Indices: 58015873--58015915 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
58015863 AGTGAGATGA
*
58015873 CAGCAAAACAATGATAAAACAG
1 CAGCAAAACAATGAGAAAACAG
*
58015895 CAGCAAAACAATGGGAAAACA
1 CAGCAAAACAATGAGAAAACA
58015916 AGAATATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.58, C:0.19, G:0.16, T:0.07
Consensus pattern (22 bp):
CAGCAAAACAATGAGAAAACAG
Found at i:58022102 original size:21 final size:21
Alignment explanation
Indices: 58022077--58022234 Score: 187
Period size: 21 Copynumber: 7.6 Consensus size: 21
58022067 CATATTTTAC
* *
58022077 TTTCTGTTTAGCTCTTACGAG
1 TTTCTGTTCAACTCTTACGAG
* *
58022098 CTTCTGTTCAACTCTTATGAG
1 TTTCTGTTCAACTCTTACGAG
58022119 TTTCTGTT-AAGCTCTTACGAG
1 TTTCTGTTCAA-CTCTTACGAG
*
58022140 TTTCTGTTCAACTCTTATGAG
1 TTTCTGTTCAACTCTTACGAG
* *
58022161 TTTCTTTTCAGCTCTTACGAG
1 TTTCTGTTCAACTCTTACGAG
*
58022182 CTTCTGTTCAACTCTTA--AG
1 TTTCTGTTCAACTCTTACGAG
* *
58022201 TTTTTGTTCAACTCTTATGAG
1 TTTCTGTTCAACTCTTACGAG
*
58022222 CTTCTGTTCAACT
1 TTTCTGTTCAACT
58022235 TTCAAGCTTC
Statistics
Matches: 116, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
19 17 0.15
20 2 0.02
21 95 0.82
22 2 0.02
ACGTcount: A:0.18, C:0.22, G:0.15, T:0.46
Consensus pattern (21 bp):
TTTCTGTTCAACTCTTACGAG
Found at i:58022125 original size:42 final size:42
Alignment explanation
Indices: 58022077--58022234 Score: 232
Period size: 42 Copynumber: 3.8 Consensus size: 42
58022067 CATATTTTAC
58022077 TTTCTGTTTAGCTCTTACGAGCTTCTGTTCAACTCTTATGAG
1 TTTCTGTTTAGCTCTTACGAGCTTCTGTTCAACTCTTATGAG
* *
58022119 TTTCTGTTAAGCTCTTACGAGTTTCTGTTCAACTCTTATGAG
1 TTTCTGTTTAGCTCTTACGAGCTTCTGTTCAACTCTTATGAG
58022161 TTTCT-TTTCAGCTCTTACGAGCTTCTGTTCAACTCTTA--AG
1 TTTCTGTTT-AGCTCTTACGAGCTTCTGTTCAACTCTTATGAG
* * * *
58022201 TTTTTGTTCAACTCTTATGAGCTTCTGTTCAACT
1 TTTCTGTTTAGCTCTTACGAGCTTCTGTTCAACT
58022235 TTCAAGCTTC
Statistics
Matches: 106, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
40 29 0.27
41 4 0.04
42 73 0.69
ACGTcount: A:0.18, C:0.22, G:0.15, T:0.46
Consensus pattern (42 bp):
TTTCTGTTTAGCTCTTACGAGCTTCTGTTCAACTCTTATGAG
Found at i:58022187 original size:63 final size:61
Alignment explanation
Indices: 58022077--58022248 Score: 206
Period size: 63 Copynumber: 2.8 Consensus size: 61
58022067 CATATTTTAC
* * * * *
58022077 TTTCTGTTTAGCTCTTACGAGCTTCTGTTCAACTCTTATGAGTTTCTGTT-AAGCTCTTACGAG
1 TTTCTGTTCAACTCTTATGAGCTTCTGTTCAACTCTTACGAGCTTCTGTTCAA-CTCTTA--AG
* * *
58022140 TTTCTGTTCAACTCTTATGAGTTTCTTTTCAGCTCTTACGAGCTTCTGTTCAACTCTTAAG
1 TTTCTGTTCAACTCTTATGAGCTTCTGTTCAACTCTTACGAGCTTCTGTTCAACTCTTAAG
* *
58022201 TTTTTGTTCAACTCTTATGAGCTTCTGTTCAACT-TT-CAAGCTTCTGTT
1 TTTCTGTTCAACTCTTATGAGCTTCTGTTCAACTCTTACGAGCTTCTGTT
58022249 GTCATATCTG
Statistics
Matches: 95, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
59 11 0.12
60 2 0.02
61 32 0.34
63 48 0.51
64 2 0.02
ACGTcount: A:0.17, C:0.22, G:0.15, T:0.47
Consensus pattern (61 bp):
TTTCTGTTCAACTCTTATGAGCTTCTGTTCAACTCTTACGAGCTTCTGTTCAACTCTTAAG
Found at i:58022738 original size:2 final size:2
Alignment explanation
Indices: 58022733--58022775 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
58022723 ATAACCAACT
58022733 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58022775 T
1 T
58022776 GGGTTTGAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:58031627 original size:3 final size:3
Alignment explanation
Indices: 58031609--58031653 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
58031599 TTTAATGAGA
*
58031609 TAT T-T TAT TAT T-T TAT TAT TAT TAT TAT TATT TAT TAT TTT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
58031653 T
1 T
58031654 TAGTATAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
2 4 0.11
3 30 0.81
4 3 0.08
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (3 bp):
TAT
Found at i:58031642 original size:19 final size:20
Alignment explanation
Indices: 58031609--58031653 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
58031599 TTTAATGAGA
58031609 TATT-TTATTATTTTATTAT
1 TATTATTATTATTTTATTAT
58031628 TATTATTATTA-TTTATTAT
1 TATTATTATTATTTTATTAT
*
58031647 TTTTATT
1 TATTATT
58031654 TAGTATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (20 bp):
TATTATTATTATTTTATTAT
Found at i:58032931 original size:51 final size:51
Alignment explanation
Indices: 58032855--58032962 Score: 207
Period size: 51 Copynumber: 2.1 Consensus size: 51
58032845 AAGTTATCCA
58032855 GATGAAATATGAAGCTCTTGTTGAAGCTAGAACAACAAAGTAATAATTCTG
1 GATGAAATATGAAGCTCTTGTTGAAGCTAGAACAACAAAGTAATAATTCTG
*
58032906 GATGAAATATGAAGCTCTTGTTGAAGCTAGAGCAACAAAGTAATAATTCTG
1 GATGAAATATGAAGCTCTTGTTGAAGCTAGAACAACAAAGTAATAATTCTG
58032957 GATGAA
1 GATGAA
58032963 GTACGAAGTA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.27
Consensus pattern (51 bp):
GATGAAATATGAAGCTCTTGTTGAAGCTAGAACAACAAAGTAATAATTCTG
Found at i:58033869 original size:46 final size:46
Alignment explanation
Indices: 58033802--58034028 Score: 355
Period size: 46 Copynumber: 4.9 Consensus size: 46
58033792 GCTTTTTGAA
*
58033802 ATGAAATATGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
58033848 ATGAATTGTGTAAGACCATGGTTGAATGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * *
58033894 ATGAAATATGTAAGACCATGGTTGAAAGATAACATGGAAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
58033940 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
** *
58033986 ATGAAATGAATAAGACCGTGGTTGAAAGATACCATGGCAACAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACAT
58034029 TATGGGGAAA
Statistics
Matches: 164, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 164 1.00
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.24
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
Found at i:58035579 original size:26 final size:26
Alignment explanation
Indices: 58035550--58035657 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
58035540 TGGTACAAAT
58035550 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
58035576 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
58035602 TGATAATGAGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
58035628 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
58035654 TGAT
1 TGAT
58035658 GGGCATTTCA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:58042224 original size:46 final size:46
Alignment explanation
Indices: 58042172--58042400 Score: 336
Period size: 46 Copynumber: 5.0 Consensus size: 46
58042162 GCTTTCTGAA
58042172 ATGAAATATGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATATGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * * *
58042218 ATGAAATGTGTAAGACCATGATTGAATGATACCATGGCAGCATGAT
1 ATGAAATATGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
58042264 ATGAAATATGTAAGACCATGGTTGAAAGATACCATGACAACATGAT
1 ATGAAATATGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * *
58042310 ATGAAATGTGTAAGACCATGGTTGGAAGATACCATGGCAACGTGACT
1 ATGAAATATGTAAGACCATGGTTGAAAGATACCATGGCAACATGA-T
* *
58042357 -TGAAATGA-ATAAGACCATGATTGAAAGATACCATGGCAACATGA
1 ATGAAAT-ATGTAAGACCATGGTTGAAAGATACCATGGCAACATGA
58042401 CGGGGAAATG
Statistics
Matches: 163, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
46 162 0.99
47 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.24
Consensus pattern (46 bp):
ATGAAATATGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
Found at i:58042447 original size:30 final size:31
Alignment explanation
Indices: 58042386--58042453 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 31
58042376 ATTGAAAGAT
* *
58042386 ACCATGGCAACATGACGGGGAAATGAATAAG
1 ACCATAGCAACATGACGGGAAAATGAATAAG
* *
58042417 ACCATAGCAACATGAC-TGAAAATGAGTAAG
1 ACCATAGCAACATGACGGGAAAATGAATAAG
58042447 ACCATAG
1 ACCATAG
58042454 TTGAAAGACA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
30 18 0.55
31 15 0.45
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (31 bp):
ACCATAGCAACATGACGGGAAAATGAATAAG
Found at i:58043193 original size:12 final size:12
Alignment explanation
Indices: 58043176--58043208 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
58043166 CGGGCCGCCC
58043176 ATATTAATTTTT
1 ATATTAATTTTT
58043188 ATATT-ATTTTT
1 ATATTAATTTTT
58043199 ATA-TAATTTT
1 ATATTAATTTT
58043209 AAAATATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:58043376 original size:30 final size:30
Alignment explanation
Indices: 58043332--58043394 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
58043322 ACTTAGCAAG
58043332 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
58043362 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
58043392 CAA
1 CAA
58043395 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:58045541 original size:13 final size:13
Alignment explanation
Indices: 58045519--58045551 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
58045509 AAGGGTTTGT
58045519 TTAT-TAAACTAA
1 TTATCTAAACTAA
58045531 TTATCTAAACTAA
1 TTATCTAAACTAA
*
58045544 TTAACTAA
1 TTATCTAA
58045552 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:58048460 original size:6 final size:6
Alignment explanation
Indices: 58048451--58048532 Score: 89
Period size: 6 Copynumber: 13.5 Consensus size: 6
58048441 AATAAAATTG
*
58048451 AAATGA AAATAA AAATAAAA AAATAA AAAT-A AAAT-A AAAT-A AAATAA
1 AAATAA AAATAA AAAT--AA AAATAA AAATAA AAATAA AAATAA AAATAA
*
58048498 AAATAA AAATAA AAATAA AATAAATA AAATAA AAA
1 AAATAA AAATAA AAATAA AA-ATA-A AAATAA AAA
58048533 GAATAAAAAG
Statistics
Matches: 68, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
5 15 0.22
6 40 0.59
7 4 0.06
8 9 0.13
ACGTcount: A:0.82, C:0.00, G:0.01, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:58048464 original size:5 final size:5
Alignment explanation
Indices: 58048441--58048540 Score: 91
Period size: 5 Copynumber: 19.4 Consensus size: 5
58048431 AAATTAAGAT
*
58048441 AATAA AATTGA AATGAA AATAA AA-ATA AA-AA AATAAA AATAA AATAA
1 AATAA AA-TAA AAT-AA AATAA AATA-A AATAA AAT-AA AATAA AATAA
*
58048488 AATAA AATAAA AATAAA AATAAA AATAA AAT-A AATAA AATAA AA-AG
1 AATAA AAT-AA AAT-AA AAT-AA AATAA AATAA AATAA AATAA AATAA
58048534 AATAA AA
1 AATAA AA
58048541 AGATAGGAGG
Statistics
Matches: 83, Mismatches: 4, Indels: 16
0.81 0.04 0.16
Matches are distributed among these distances:
4 11 0.13
5 42 0.51
6 30 0.36
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
AATAA
Found at i:58048492 original size:47 final size:46
Alignment explanation
Indices: 58048441--58048540 Score: 139
Period size: 47 Copynumber: 2.2 Consensus size: 46
58048431 AAATTAAGAT
** *
58048441 AATAAAATTGAAATGAAAATAAAAATAAAA-AAATAAAAATAAAATAA
1 AATAAAATAAAAATAAAAATAAAAATAAAATAAAT-AAAATAAAA-AA
*
58048488 AATAAAATAAAAATAAAAATAAAAATAAAATAAATAAAATAAAAAG
1 AATAAAATAAAAATAAAAATAAAAATAAAATAAATAAAATAAAAAA
58048534 AATAAAA
1 AATAAAA
58048541 AGATAGGAGG
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
46 8 0.17
47 36 0.75
48 4 0.08
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (46 bp):
AATAAAATAAAAATAAAAATAAAAATAAAATAAATAAAATAAAAAA
Found at i:58053942 original size:13 final size:13
Alignment explanation
Indices: 58053920--58053952 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
58053910 AAGGGTTTGT
58053920 TTAT-TAAACTAA
1 TTATCTAAACTAA
58053932 TTATCTAAACTAA
1 TTATCTAAACTAA
*
58053945 TTAACTAA
1 TTATCTAA
58053953 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:58062317 original size:28 final size:28
Alignment explanation
Indices: 58062248--58062348 Score: 105
Period size: 28 Copynumber: 3.5 Consensus size: 28
58062238 GACAAGATTG
* * * *
58062248 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
58062278 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
58062306 GCACTAAGTGTGCGAG-CTGAATGTATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
*
58062335 ACACTAAGTGTGCG
1 GCACTAAGTGTGCG
58062349 GATTCACTAT
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
27 2 0.03
28 24 0.38
29 19 0.30
30 18 0.29
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:58062342 original size:29 final size:28
Alignment explanation
Indices: 58062279--58062348 Score: 97
Period size: 29 Copynumber: 2.5 Consensus size: 28
58062269 AATTGTACAG
* *
58062279 CACTAAGTGTGCGAGTTTGATTATATAG
1 CACTAAGTGTGCGAGTCTGATTATATAA
58062307 CACTAAGTGTGCGAG-CTGAATGTATATAA
1 CACTAAGTGTGCGAGTCTG-AT-TATATAA
58062336 CACTAAGTGTGCG
1 CACTAAGTGTGCG
58062349 GATTCACTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 2 0.05
28 17 0.45
29 19 0.50
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTCTGATTATATAA
Found at i:58067047 original size:38 final size:39
Alignment explanation
Indices: 58066914--58067035 Score: 228
Period size: 39 Copynumber: 3.2 Consensus size: 39
58066904 GCTCTGATGA
58066914 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
*
58066953 GCTTCAGTTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
58066992 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCAC-TATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
58067030 GCTTCA
1 GCTTCA
58067036 ACTAGATTTC
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
38 11 0.14
39 70 0.86
ACGTcount: A:0.13, C:0.27, G:0.23, T:0.37
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
Found at i:58068396 original size:31 final size:31
Alignment explanation
Indices: 58068358--58068418 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
58068348 ACAAATGACA
***
58068358 AGTGAAAAGTAGTAGTTTCGGCTACCTGATC
1 AGTGAAAAGTAGTAGCACCGGCTACCTGATC
*
58068389 AGTGAAAAGTGGTAGCACCGGCTACCTGAT
1 AGTGAAAAGTAGTAGCACCGGCTACCTGAT
58068419 AGATAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.25
Consensus pattern (31 bp):
AGTGAAAAGTAGTAGCACCGGCTACCTGATC
Found at i:58068492 original size:69 final size:71
Alignment explanation
Indices: 58068389--58068532 Score: 247
Period size: 70 Copynumber: 2.1 Consensus size: 71
58068379 CTACCTGATC
*
58068389 AGTGAAAAGTGGTAGCACCGGCTACCTGATAGAT-AAAAAAATGGTCGCTCTGGCTACCTAATCA
1 AGTGAAAAGTGGTAGCACCGGCTACCTGATAGATAAAAAAAATGGTAGCTCTGGCTACCTAATCA
58068453 GTGAAT
66 GTGAAT
* *
58068459 AGTGAAAAGTGGTAGC-TCGGCTACCTGATAGATAAAAAAAATGGTAGCTCTGGCTACCTGATCA
1 AGTGAAAAGTGGTAGCACCGGCTACCTGATAGATAAAAAAAATGGTAGCTCTGGCTACCTAATCA
58068523 GTGAAT
66 GTGAAT
58068529 AGTG
1 AGTG
58068533 GTAGCTTCGG
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
69 16 0.23
70 54 0.77
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.24
Consensus pattern (71 bp):
AGTGAAAAGTGGTAGCACCGGCTACCTGATAGATAAAAAAAATGGTAGCTCTGGCTACCTAATCA
GTGAAT
Found at i:58068507 original size:32 final size:33
Alignment explanation
Indices: 58068393--58068520 Score: 127
Period size: 32 Copynumber: 3.8 Consensus size: 33
58068383 CTGATCAGTG
* * *
58068393 AAAAGTGGTAGCACCGGCTACCTGATAGAT-AA
1 AAAAATGGTAGCTCTGGCTACCTGATAGATAAA
* *
58068425 AAAAATGGTCGCTCTGGCTACCTAATCAG-TGAATA
1 AAAAATGGTAGCTCTGGCTACCTGAT-AGAT-AA-A
*
58068460 GTGAAAAGTGGTAGCTC-GGCTACCTGATAGATAAA
1 ---AAAAATGGTAGCTCTGGCTACCTGATAGATAAA
58068495 AAAAATGGTAGCTCTGGCTACCTGAT
1 AAAAATGGTAGCTCTGGCTACCTGAT
58068521 CAGTGAATAG
Statistics
Matches: 78, Mismatches: 9, Indels: 17
0.75 0.09 0.16
Matches are distributed among these distances:
32 35 0.45
33 13 0.17
34 1 0.01
35 2 0.03
36 4 0.05
37 11 0.14
38 12 0.15
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.23
Consensus pattern (33 bp):
AAAAATGGTAGCTCTGGCTACCTGATAGATAAA
Found at i:58068538 original size:31 final size:30
Alignment explanation
Indices: 58068457--58068546 Score: 94
Period size: 31 Copynumber: 2.9 Consensus size: 30
58068447 TAATCAGTGA
58068457 ATAGTGAAAAGTGGTAGCTC-GGCTACCTG
1 ATAGTGAAAAGTGGTAGCTCTGGCTACCTG
* *
58068486 ATAGATAAAAAAAATGGTAGCTCTGGCTACCTG
1 ATAG-T--GAAAAGTGGTAGCTCTGGCTACCTG
*
58068519 ATCAGTGAATAGTGGTAGCT-TCGGCTAC
1 AT-AGTGAAAAGTGGTAGCTCT-GGCTAC
58068547 AAGTGACAAG
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
29 4 0.08
30 2 0.04
31 17 0.34
32 13 0.26
33 12 0.24
34 2 0.04
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.26
Consensus pattern (30 bp):
ATAGTGAAAAGTGGTAGCTCTGGCTACCTG
Found at i:58072052 original size:39 final size:39
Alignment explanation
Indices: 58071879--58072057 Score: 295
Period size: 39 Copynumber: 4.6 Consensus size: 39
58071869 GCTCTGATGA
58071879 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
*
58071918 GCTTCAGTTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
*
58071957 GCTTCAGTTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
* *
58071996 GCTTTAGTTAGCCTTCGGGCTTCCGTTTAGCACGTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
* **
58072035 GCTTCAGCTAGATTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
58072058 AGATCACGAT
Statistics
Matches: 132, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 132 1.00
ACGTcount: A:0.13, C:0.26, G:0.24, T:0.37
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
Found at i:58089712 original size:14 final size:15
Alignment explanation
Indices: 58089683--58089713 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
58089673 ATTCTTTAAA
58089683 AACTATAAAAATATT
1 AACTATAAAAATATT
58089698 AACTATAAAAA-ATT
1 AACTATAAAAATATT
58089712 AA
1 AA
58089714 AATTTCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (15 bp):
AACTATAAAAATATT
Found at i:58095587 original size:18 final size:20
Alignment explanation
Indices: 58095542--58095588 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
58095532 AATTGGTATA
58095542 AAGTGCATATCTGGCACATG
1 AAGTGCATATCTGGCACATG
* *
58095562 AGGTGCAT-TTTGGCACAT-
1 AAGTGCATATCTGGCACATG
58095580 AAGTGCATA
1 AAGTGCATA
58095589 ATCCTATACA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 7 0.30
19 9 0.39
20 7 0.30
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.28
Consensus pattern (20 bp):
AAGTGCATATCTGGCACATG
Found at i:58108096 original size:24 final size:24
Alignment explanation
Indices: 58108062--58108108 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
58108052 ATTAATTGTA
* *
58108062 AAAAAATTATATACTGGATCCAAT
1 AAAAAACTATATACCGGATCCAAT
58108086 AAAAAACTATATACCGGATCCAA
1 AAAAAACTATATACCGGATCCAA
58108109 GATTTTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.51, C:0.17, G:0.09, T:0.23
Consensus pattern (24 bp):
AAAAAACTATATACCGGATCCAAT
Found at i:58108888 original size:27 final size:27
Alignment explanation
Indices: 58108853--58108904 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
58108843 AAAATTTTTT
* *
58108853 AATATATTTGATATTATTAGAAATAAC
1 AATAAATTTAATATTATTAGAAATAAC
*
58108880 AATAAATTTAATATTGTTAGAAATA
1 AATAAATTTAATATTATTAGAAATA
58108905 GACTATTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (27 bp):
AATAAATTTAATATTATTAGAAATAAC
Found at i:58111794 original size:64 final size:64
Alignment explanation
Indices: 58111693--58111851 Score: 255
Period size: 64 Copynumber: 2.5 Consensus size: 64
58111683 TGAGCTTATG
* * * *
58111693 TAATTTATATAAAAAAAAATTACATTACAAAATTTGTTCCAATTAGATTATGGTTGTAATGTATT
1 TAATTTATAT-AAAATAATTTATATTACAAAATTTGTTCCAATTAGATTATGGTTGTAATGAATT
*
58111758 TAATTTATATAAAATAATTTATATTACAAACTTTGTTCCAATTAGATTATGGTTGTAATGAATT
1 TAATTTATATAAAATAATTTATATTACAAAATTTGTTCCAATTAGATTATGGTTGTAATGAATT
*
58111822 TAATTTATATAACATAATTTATATTACAAA
1 TAATTTATATAAAATAATTTATATTACAAA
58111852 GCTAAGTTTG
Statistics
Matches: 88, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
64 78 0.89
65 10 0.11
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (64 bp):
TAATTTATATAAAATAATTTATATTACAAAATTTGTTCCAATTAGATTATGGTTGTAATGAATT
Found at i:58114357 original size:114 final size:110
Alignment explanation
Indices: 58114206--58114424 Score: 309
Period size: 107 Copynumber: 2.0 Consensus size: 110
58114196 CCACATTAAA
*
58114206 ATATTAAAATACTAAAAATAATATGCCAATAAAAAAAATAAAAAACATAACATAAACGATACATA
1 ATATTAAAATACTAAAAATAACATGCCAAT------AA-AAAAAACATAACATAAACGATACATA
** *
58114271 ATAAATA-TGA-ATTTTT-TTATTATTTTAAAATGATAATAAGTAAATTTTT
59 ATAAATACAAATATTTTTATTATTACTTTAAAATGATAATAAGTAAATTTTT
*
58114320 ATATTAAAATACTAAAAATAACATGCCAATAACAAAAACATAACATAAACGATACATAATAAATA
1 ATATTAAAATACTAAAAATAACATGCCAATAAAAAAAACATAACATAAACGATACATAATAAATA
58114385 CAAATATTTTTATTATTACTTTAAAATGATAATAAGTAAA
66 CAAATATTTTTATTATTACTTTAAAATGATAATAAGTAAA
58114425 CATTTTTGGT
Statistics
Matches: 97, Mismatches: 5, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
107 32 0.33
108 3 0.03
109 6 0.06
110 27 0.28
114 29 0.30
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.32
Consensus pattern (110 bp):
ATATTAAAATACTAAAAATAACATGCCAATAAAAAAAACATAACATAAACGATACATAATAAATA
CAAATATTTTTATTATTACTTTAAAATGATAATAAGTAAATTTTT
Found at i:58115115 original size:15 final size:15
Alignment explanation
Indices: 58115083--58115122 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
58115073 CTCCTTCTTC
*
58115083 TTCTTCT-CTT-CTT
1 TTCTTCTCCTTCCCT
58115096 TTCTTCTCCTTCCCT
1 TTCTTCTCCTTCCCT
58115111 TTCTTCTCCTTC
1 TTCTTCTCCTTC
58115123 ACCCACTAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 7 0.29
14 3 0.12
15 14 0.58
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (15 bp):
TTCTTCTCCTTCCCT
Found at i:58115827 original size:20 final size:20
Alignment explanation
Indices: 58115786--58115840 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
58115776 GTTTAGTGTT
*
58115786 TTTTTTATA-TTTTTAAGTA
1 TTTTTTATATTTTTTAAGAA
58115805 TTTTTATATATTTTTTAA-AA
1 TTTTT-TATATTTTTTAAGAA
58115825 TTTTTTATAATTTTTT
1 TTTTTTAT-ATTTTTT
58115841 GAGTTGTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
19 8 0.25
20 17 0.53
21 7 0.22
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTTTTATATTTTTTAAGAA
Found at i:58116384 original size:14 final size:16
Alignment explanation
Indices: 58116361--58116393 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
58116351 TTTTTGGTCA
58116361 TTTCTATCTTTTTC-T
1 TTTCTATCTTTTTCAT
58116376 TTTCT-TCTTTTTCAT
1 TTTCTATCTTTTTCAT
58116391 TTT
1 TTT
58116394 GATTATTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTCTATCTTTTTCAT
Found at i:58117753 original size:2 final size:2
Alignment explanation
Indices: 58117746--58117775 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
58117736 CTGAAGTTGC
58117746 AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
58117776 ACTCATTTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58128984 original size:9 final size:9
Alignment explanation
Indices: 58128955--58128986 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
58128945 TAAGTTTTCG
58128955 AATTCGAAT
1 AATTCGAAT
*
58128964 AACTCGAAT
1 AATTCGAAT
58128973 AATTCGAAT
1 AATTCGAAT
58128982 AATTC
1 AATTC
58128987 AACTATCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (9 bp):
AATTCGAAT
Found at i:58129363 original size:19 final size:19
Alignment explanation
Indices: 58129336--58129373 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
58129326 TCCCTCAAAC
58129336 TTTTATTCC-ACAACTTTTA
1 TTTTATTCCTA-AACTTTTA
*
58129355 TTTTCTTCCTAAACTTTTA
1 TTTTATTCCTAAACTTTTA
58129374 CTTCTCACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.24, C:0.21, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTTATTCCTAAACTTTTA
Found at i:58133053 original size:116 final size:116
Alignment explanation
Indices: 58132849--58133082 Score: 441
Period size: 116 Copynumber: 2.0 Consensus size: 116
58132839 AGGAGTGCTT
*
58132849 ATAAACTACTACAGGAGGCTAATTCGGGTCCCAGTGATAATTTTTTACAGGCCAAGACTAGAGAT
1 ATAAACTACTACAAGAGGCTAATTCGGGTCCCAGTGATAATTTTTTACAGGCCAAGACTAGAGAT
58132914 TTCTGTAGGAAATTATGGAATATACATCTCCCTTCAAAAATTAAATTAACA
66 TTCTGTAGGAAATTATGGAATATACATCTCCCTTCAAAAATTAAATTAACA
* *
58132965 ATAAACTACTACAAGAGGCTAATTCGGGTCCTAGTGATAATTTTTTACAGGCCGAGACTAGAGAT
1 ATAAACTACTACAAGAGGCTAATTCGGGTCCCAGTGATAATTTTTTACAGGCCAAGACTAGAGAT
58133030 TTCTGTAGGAAATTATGGAATATACATCTCCCTTCAAAAATTAAATTAACA
66 TTCTGTAGGAAATTATGGAATATACATCTCCCTTCAAAAATTAAATTAACA
58133081 AT
1 AT
58133083 TTGGAGAATT
Statistics
Matches: 115, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
116 115 1.00
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (116 bp):
ATAAACTACTACAAGAGGCTAATTCGGGTCCCAGTGATAATTTTTTACAGGCCAAGACTAGAGAT
TTCTGTAGGAAATTATGGAATATACATCTCCCTTCAAAAATTAAATTAACA
Found at i:58135609 original size:30 final size:30
Alignment explanation
Indices: 58135575--58135633 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
58135565 TGTTTTATTG
58135575 TTAATTTTGTTATTATTTTAGAAGCATTTC
1 TTAATTTTGTTATTATTTTAGAAGCATTTC
*
58135605 TTAATTTTGTTATTATTTTAGAGGCATTT
1 TTAATTTTGTTATTATTTTAGAAGCATTT
58135634 GTTTGTTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.05, G:0.12, T:0.58
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAGAAGCATTTC
Found at i:58136193 original size:2 final size:2
Alignment explanation
Indices: 58136186--58136233 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
58136176 TTTGAATAGG
58136186 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
58136228 AT AT AT
1 AT AT AT
58136234 GTGTGTGTGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58150417 original size:2 final size:2
Alignment explanation
Indices: 58150400--58150446 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
58150390 GTTATCAAAA
* *
58150400 AG AG AA AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
58150442 A- AG AG
1 AG AG AG
58150447 GGTCACAGCT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:58152995 original size:16 final size:16
Alignment explanation
Indices: 58152976--58153009 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
58152966 AAAAAAAAGG
58152976 AAAAAAGAAAAGAAAA
1 AAAAAAGAAAAGAAAA
58152992 AAAAAAGAAAAGAAAA
1 AAAAAAGAAAAGAAAA
58153008 AA
1 AA
58153010 TGGAGAGGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAAGAAAA
Found at i:58154028 original size:44 final size:44
Alignment explanation
Indices: 58153978--58154273 Score: 174
Period size: 44 Copynumber: 6.8 Consensus size: 44
58153968 GATCCAAGAT
* * *
58153978 GATTTGGCGTCTCTGTATTGTCAGGGAGCAGATAAAAAATGACA
1 GATTTGGCATCTCTGTATTGGCAGGGAGCAGATAAAAAATAACA
* ** *
58154022 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
1 GATTTGGCATCTCTGTATTGGCAGGGAGCAGATAAAAAATAACA
* * *
58154066 AATTTGGCATCTCTGTATTGGCAGGGAGCAGATCGAAGACATAACTA
1 GATTTGGCATCTCTGTATTGGCAGGGAGCAGAT--AAAAAATAAC-A
* * * * * * ** *
58154113 -ATTTGGCTTTCACGTGT-TT-ACATTGAAGCAAATCCAAGAT----
1 GATTTGGC-ATCTC-TGTATTGGCA-GGGAGCAGATAAAAAATAACA
* * * * ** * *
58154153 GATTTGGCGTATCTGTATTGTCAGAGAGCAGATCGAAGATAGCA
1 GATTTGGCATCTCTGTATTGGCAGGGAGCAGATAAAAAATAACA
* * ** * *
58154197 GATTTGGCATCTCTGTATTGGCAGAGAGCCGATCGAAAACAGCA
1 GATTTGGCATCTCTGTATTGGCAGGGAGCAGATAAAAAATAACA
* *
58154241 GATTTGGCGTCTCTATATTGGCAGGGAGCAGAT
1 GATTTGGCATCTCTGTATTGGCAGGGAGCAGAT
58154274 CAAGGACATA
Statistics
Matches: 197, Mismatches: 42, Indels: 26
0.74 0.16 0.10
Matches are distributed among these distances:
39 3 0.02
40 16 0.08
41 9 0.05
44 135 0.69
45 3 0.02
46 15 0.08
47 13 0.07
48 3 0.02
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (44 bp):
GATTTGGCATCTCTGTATTGGCAGGGAGCAGATAAAAAATAACA
Found at i:58154182 original size:87 final size:87
Alignment explanation
Indices: 58154067--58154708 Score: 644
Period size: 87 Copynumber: 7.5 Consensus size: 87
58154057 AAGATAACAA
* * *
58154067 ATTTGGCATCTCTGTATTGGCAGGGAGCAGATCGAAGACATAACTAATTTGGCTTTCACGTGTTT
1 ATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTT
* *
58154132 ACATTGAAGCAAATCCAAGATG
66 ACGTTGAAGCAAATCTAAGATG
* * * * * *
58154154 ATTTGGCGTATCTGTATTGTCAGAGAGCAGATCGAAG--ATAGCAGATTTGGC-ATCTC-TGTAT
1 ATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGT-T
* ** ** *
58154215 T-GGCAGAGAGCCGATCGAAAACAGCA-G
65 TACGTTGA-AGCAAATC---TA-AG-ATG
*
58154242 ATTTGGCGTCTCTATATTGGCAGGGAGCAGATC-AAGGACATAGCTGATTTGGCTTTCACGTGTT
1 ATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAA-GACATAGCTGATTTGGCTTTCACGTGTT
58154306 TACGTTGAAGCAAATCTAAGATG
65 TACGTTGAAGCAAATCTAAGATG
58154329 ATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTT
1 ATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTT
58154394 ACGTTGAAGCAAATCTAAGATG
66 ACGTTGAAGCAAATCTAAGATG
* * * * * * * * *
58154416 ATTTGACATCTCTGTATTGGCAGAGAACAAATTGAAGAC--AGATGATTTGG-TGTCTC-TGTAT
1 ATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGT-T
* * * *
58154477 T--GTCAAGGAGCAGATCGAAGATACCAG
65 TACGT--TGAAGCAAATCTAAGAT----G
*
58154504 ATTTGGTGTCTCTGTATTGGCAGGGAGCAGATCGAAGAC--A--T-A----GCTTTCACGTGTTT
1 ATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTT
58154560 ACGTTGAAGCAAATCTAAGATG
66 ACGTTGAAGCAAATCTAAGATG
* * * *
58154582 ATTTGGCGTCTCTGTATTGGCAGGGAGCAGATTGAAGACGTAGTTGATTTGGTTTTCACGTGTTT
1 ATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTT
*
58154647 ACGTTGAAGTAAATCTAAGATG
66 ACGTTGAAGCAAATCTAAGATG
* *
58154669 ATTTGGCGTCTTTGTATTGGCAGAGAGCAGATCGAAGACA
1 ATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACA
58154709 GATGATTTGG
Statistics
Matches: 456, Mismatches: 64, Indels: 70
0.77 0.11 0.12
Matches are distributed among these distances:
78 38 0.08
80 1 0.00
81 1 0.00
82 22 0.05
83 12 0.03
84 32 0.07
85 22 0.05
86 2 0.00
87 225 0.49
88 70 0.15
89 1 0.00
90 13 0.03
91 11 0.02
92 6 0.01
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (87 bp):
ATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTT
ACGTTGAAGCAAATCTAAGATG
Found at i:58154262 original size:175 final size:175
Alignment explanation
Indices: 58153954--58154381 Score: 626
Period size: 175 Copynumber: 2.4 Consensus size: 175
58153944 CCTTCAAGTA
* * ** *
58153954 TTTACACTGAAGCAGATCCAAGATGATTTGGCGTCTCTGTATTGTCAGGGAGCAGATAAAAAAT-
1 TTTACATTGAAGCAAATCCAAGATGATTTGGCGTCTCTGTATTGTCAGGGAGCAGATCGAAGATA
* * *
58154018 GACAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACAAATTTGGCATCTCTGTA
66 G-CAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAAACAACAAATTTGGCATCTCTATA
58154083 TTGGCAGGGAGCAGATCGAA-GACATAACTAATTTGGCTTTCACGTG
130 TTGGCAGGGAGCAGATC-AAGGACATAACTAATTTGGCTTTCACGTG
* *
58154129 TTTACATTGAAGCAAATCCAAGATGATTTGGCGTATCTGTATTGTCAGAGAGCAGATCGAAGATA
1 TTTACATTGAAGCAAATCCAAGATGATTTGGCGTCTCTGTATTGTCAGGGAGCAGATCGAAGATA
* * * *
58154194 GCAGATTTGGCATCTCTGTATTGGCAGAGAGCCGATCGAAAACAGCAGATTTGGCGTCTCTATAT
66 GCAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAAACAACAAATTTGGCATCTCTATAT
* *
58154259 TGGCAGGGAGCAGATCAAGGACATAGCTGATTTGGCTTTCACGTG
131 TGGCAGGGAGCAGATCAAGGACATAACTAATTTGGCTTTCACGTG
* * *
58154304 TTTACGTTGAAGCAAATCTAAGATGATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACA
1 TTTACATTGAAGCAAATCCAAGATGATTTGGCGTCTCTGTATTGTCAGGGAGCAGATCGAAG--A
*
58154369 TAGCTGATTTGGC
64 TAGCAGATTTGGC
58154382 TTTCACGTGT
Statistics
Matches: 227, Mismatches: 22, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
174 2 0.01
175 211 0.93
176 1 0.00
177 13 0.06
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (175 bp):
TTTACATTGAAGCAAATCCAAGATGATTTGGCGTCTCTGTATTGTCAGGGAGCAGATCGAAGATA
GCAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAAACAACAAATTTGGCATCTCTATAT
TGGCAGGGAGCAGATCAAGGACATAACTAATTTGGCTTTCACGTG
Found at i:58154497 original size:44 final size:44
Alignment explanation
Indices: 58154424--58154543 Score: 145
Period size: 44 Copynumber: 2.7 Consensus size: 44
58154414 TGATTTGACA
* * * *
58154424 TCTCTGTATTGGC-AGAGAACAAATTGAAGACA-GATGATTTGGTG
1 TCTCTGTATTGGCAAG-GAGCAGATCGAAGACACCA-GATTTGGTG
* *
58154468 TCTCTGTATTGTCAAGGAGCAGATCGAAGATACCAGATTTGGTG
1 TCTCTGTATTGGCAAGGAGCAGATCGAAGACACCAGATTTGGTG
*
58154512 TCTCTGTATTGGCAGGGAGCAGATCGAAGACA
1 TCTCTGTATTGGCAAGGAGCAGATCGAAGACA
58154544 TAGCTTTCAC
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
44 62 0.95
45 3 0.05
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (44 bp):
TCTCTGTATTGGCAAGGAGCAGATCGAAGACACCAGATTTGGTG
Found at i:58154532 original size:262 final size:253
Alignment explanation
Indices: 58154067--58154800 Score: 960
Period size: 253 Copynumber: 2.9 Consensus size: 253
58154057 AAGATAACAA
* * *
58154067 ATTTGGCATCTCTGTATTGGCAGGGAGCAGATCGAAGACATAACTAATTTGGCTTTCACGTGTTT
1 ATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTT
* * * * *
58154132 ACATTGAAGCAAATCCAAGATGATTTGGCGTATCTGTATTGTCAGAGAGCAGATCGAAGATAGCA
66 ACGTTGAAGCAAATCTAAGATGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGACAG-A
* * *
58154197 -GATTTGGCATCTCTGTATTGGCAGAGAGCCGATCGAAAACAGCAGATTTGGCGTCTCTATATTG
130 TGATTTGGTATCTCTGTATTGGCAGAGAGCAGATCGAAAACACCAGATTTGGCGTCTCTATATTG
58154261 GCAGGGAGCAGATC-AAGGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCTAA
195 GCAGGGAGCAGATCGAA-GAC--A--T-A----GCTTTCACGTGTTTACGTTGAAGCAAATCTAA
58154325 GATG
250 GATG
58154329 ATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTT
1 ATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTT
* * * * *
58154394 ACGTTGAAGCAAATCTAAGATGATTTGACATCTCTGTATTGGCAGAGAACAAATTGAAGACAGAT
66 ACGTTGAAGCAAATCTAAGATGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGACAGAT
* * * * * *
58154459 GATTTGGTGTCTCTGTATTGTCA-AGGAGCAGATCGAAGATACCAGATTTGGTGTCTCTGTATTG
131 GATTTGGTATCTCTGTATTGGCAGA-GAGCAGATCGAAAACACCAGATTTGGCGTCTCTATATTG
58154523 GCAGGGAGCAGATCGAAGACATAGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATG
195 GCAGGGAGCAGATCGAAGACATAGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATG
* * * *
58154582 ATTTGGCGTCTCTGTATTGGCAGGGAGCAGATTGAAGACGTAGTTGATTTGGTTTTCACGTGTTT
1 ATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTT
* *
58154647 ACGTTGAAGTAAATCTAAGATGATTTGGCGTCTTTGTATTGGCAGAGAGCAGATCGAAGACAGAT
66 ACGTTGAAGCAAATCTAAGATGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGACAGAT
* * * * * *
58154712 GATTTGGTATCTTTGTATTGCCAGAGAACA-ATTTGAAGAA-A-CAGATTTGGCATCTCCATATT
131 GATTTGGTATCTCTGTATTGGCAGAGAGCAGA-TCGAA-AACACCAGATTTGGCGTCTCTATATT
*
58154774 CG-ACGGAGAGCAGATCGAAGACATAGC
194 GGCA-GG-GAGCAGATCGAAGACATAGC
58154801 AGATCTAACC
Statistics
Matches: 420, Mismatches: 44, Indels: 25
0.86 0.09 0.05
Matches are distributed among these distances:
251 1 0.00
252 21 0.05
253 204 0.49
254 2 0.00
257 1 0.00
258 1 0.00
260 1 0.00
261 2 0.00
262 185 0.44
263 2 0.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (253 bp):
ATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTT
ACGTTGAAGCAAATCTAAGATGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGACAGAT
GATTTGGTATCTCTGTATTGGCAGAGAGCAGATCGAAAACACCAGATTTGGCGTCTCTATATTGG
CAGGGAGCAGATCGAAGACATAGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATG
Found at i:58154663 original size:253 final size:257
Alignment explanation
Indices: 58154067--58154738 Score: 953
Period size: 262 Copynumber: 2.6 Consensus size: 257
58154057 AAGATAACAA
* * *
58154067 ATTTGGCATCTCTGTATTGGCAGGGAGCAGATCGAAGACATAACTAATTTGGCTTTCACGTGTTT
1 ATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTT
* * * * *
58154132 ACATTGAAGCAAATCCAAGATGATTTGGCGTATCTGTATTGTCAGAGAGCAGATCGAAGATAGCA
66 ACGTTGAAGCAAATCTAAGATGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGACAG-A
* * *
58154197 -GATTTGGCATCTCTGTATTGGCAGAGAGCCGATCGAAAACAGCAGATTTGGCGTCTCTATATTG
130 TGATTTGGTATCTCTGTATTGGCAGAGAGCAGATCGAAAACACCAGATTTGGCGTCTCTATATTG
58154261 GCAGGGAGCAGATCAAGGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCTAAG
195 GCAGGGAGCAGATCAAGGACA-A-CTGA--T-GCTTTCACGTGTTTACGTTGAAGCAAATCTAAG
58154326 ATG
255 ATG
58154329 ATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTT
1 ATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTT
* * * * *
58154394 ACGTTGAAGCAAATCTAAGATGATTTGACATCTCTGTATTGGCAGAGAACAAATTGAAGACAGAT
66 ACGTTGAAGCAAATCTAAGATGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGACAGAT
* * * * * *
58154459 GATTTGGTGTCTCTGTATTGTCA-AGGAGCAGATCGAAGATACCAGATTTGGTGTCTCTGTATTG
131 GATTTGGTATCTCTGTATTGGCAGA-GAGCAGATCGAAAACACCAGATTTGGCGTCTCTATATTG
58154523 GCAGGGAGCAGATCGAA-GAC-A-T-A-GCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATG
195 GCAGGGAGCAGATC-AAGGACAACTGATGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATG
* * * *
58154582 ATTTGGCGTCTCTGTATTGGCAGGGAGCAGATTGAAGACGTAGTTGATTTGGTTTTCACGTGTTT
1 ATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTT
* *
58154647 ACGTTGAAGTAAATCTAAGATGATTTGGCGTCTTTGTATTGGCAGAGAGCAGATCGAAGACAGAT
66 ACGTTGAAGCAAATCTAAGATGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGACAGAT
* *
58154712 GATTTGGTATCTTTGTATTGCCAGAGA
131 GATTTGGTATCTCTGTATTGGCAGAGA
58154739 ACAATTTGAA
Statistics
Matches: 370, Mismatches: 36, Indels: 17
0.87 0.09 0.04
Matches are distributed among these distances:
253 177 0.48
254 1 0.00
257 1 0.00
258 1 0.00
260 1 0.00
261 2 0.01
262 185 0.50
263 2 0.01
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.31
Consensus pattern (257 bp):
ATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTT
ACGTTGAAGCAAATCTAAGATGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGACAGAT
GATTTGGTATCTCTGTATTGGCAGAGAGCAGATCGAAAACACCAGATTTGGCGTCTCTATATTGG
CAGGGAGCAGATCAAGGACAACTGATGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATG
Found at i:58154750 original size:44 final size:44
Alignment explanation
Indices: 58154664--58154766 Score: 120
Period size: 44 Copynumber: 2.4 Consensus size: 44
58154654 AGTAAATCTA
* * *
58154664 AGATGATTTGGCGTCTTTGTATTGGCAGAGAGCAGATCGAAGAC
1 AGATGATTTGGCATCTTTGTATTGCCAGAGAACAGATCGAAGAC
* * *
58154708 AGATGATTTGGTATCTTTGTATTGCCAGAGAACA-ATTTGAAGAA
1 AGATGATTTGGCATCTTTGTATTGCCAGAGAACAGA-TCGAAGAC
*
58154752 ACA-GATTTGGCATCT
1 AGATGATTTGGCATCT
58154767 CCATATTCGA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
43 12 0.24
44 38 0.76
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.31
Consensus pattern (44 bp):
AGATGATTTGGCATCTTTGTATTGCCAGAGAACAGATCGAAGAC
Found at i:58154985 original size:44 final size:43
Alignment explanation
Indices: 58154937--58155186 Score: 191
Period size: 44 Copynumber: 5.6 Consensus size: 43
58154927 GATTTTAACA
* * *
58154937 TGGCATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAGCATATT
1 TGGCATCCCTGTGTTTACAGGGAACAGA-TCGAAGATAGCAGA-T
*
58154981 TGGCATCCCTGTGTTTACAGAGAACAGATCGAAGACATAGCAGAT
1 TGGCATCCCTGTGTTTACAGGGAACAGATCGAAG--ATAGCAGAT
** * * * **
58155026 CTGATATTCCTGTGCTTACAGCGAAGCAGATCGAAGATTTCAGCA-
1 -TGGCATCCCTGTGTTTACAGGGAA-CAGATCGAAGATAGCAG-AT
*
58155071 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGACATAGCAGAT
1 TGGCATCCCTGTGTTTACAGGGAACAGATCGAAG--ATAGCAGAT
* * * * * **
58155116 CTGACATTCCTGTGCTTACAGCGAAGCAGATTGAAGATTTCAG-T
1 -TGGCATCCCTGTGTTTACAGGGAA-CAGATCGAAGATAGCAGAT
*
58155160 ATGGCATCCCTGTGTTTATAGGGAACA
1 -TGGCATCCCTGTGTTTACAGGGAACA
58155187 AGTTGAAGAA
Statistics
Matches: 162, Mismatches: 33, Indels: 23
0.74 0.15 0.11
Matches are distributed among these distances:
43 12 0.07
44 68 0.42
45 17 0.10
46 46 0.28
47 19 0.12
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (43 bp):
TGGCATCCCTGTGTTTACAGGGAACAGATCGAAGATAGCAGAT
Found at i:58155045 original size:46 final size:47
Alignment explanation
Indices: 58154869--58155152 Score: 200
Period size: 44 Copynumber: 6.3 Consensus size: 47
58154859 GTTTACAAAG
*
58154869 AGCAAATCGAAGACATAGCAGATCTGACATTCCTGTGCTTACAGCGA
1 AGCAGATCGAAGACATAGCAGATCTGACATTCCTGTGCTTACAGCGA
* * *** * * * * *
58154916 GGCAGATC-AA-AGATTTTA-A-CATGGCATCCCTGTGTTTATAGGGA
1 AGCAGATCGAAGACATAGCAGATC-TGACATTCCTGTGCTTACAGCGA
* * * * * * *
58154960 A-CA-AGTTGAAG--ATAGCATATTTGGCATCCCTGTGTTTACAGAGA
1 AGCAGA-TCGAAGACATAGCAGATCTGACATTCCTGTGCTTACAGCGA
*
58155004 A-CAGATCGAAGACATAGCAGATCTGATATTCCTGTGCTTACAGCGA
1 AGCAGATCGAAGACATAGCAGATCTGACATTCCTGTGCTTACAGCGA
** * * * * *
58155050 AGCAGATCGAAG--ATTTCAG--CATGGCATCCCTGTGTTTATAGGGA
1 AGCAGATCGAAGACATAGCAGATC-TGACATTCCTGTGCTTACAGCGA
58155094 A-CAGATCGAAGACATAGCAGATCTGACATTCCTGTGCTTACAGCGA
1 AGCAGATCGAAGACATAGCAGATCTGACATTCCTGTGCTTACAGCGA
*
58155140 AGCAGATTGAAGA
1 AGCAGATCGAAGA
58155153 TTTCAGTATG
Statistics
Matches: 178, Mismatches: 43, Indels: 32
0.70 0.17 0.13
Matches are distributed among these distances:
42 1 0.01
43 18 0.10
44 69 0.39
45 15 0.08
46 48 0.27
47 27 0.15
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (47 bp):
AGCAGATCGAAGACATAGCAGATCTGACATTCCTGTGCTTACAGCGA
Found at i:58155105 original size:134 final size:135
Alignment explanation
Indices: 58154843--58155152 Score: 426
Period size: 134 Copynumber: 2.3 Consensus size: 135
58154833 GATCCAAGAT
* * * *
58154843 GATTTGGCATTCTTGTGTTTACAAAGAGCAAATCGAAGACATAGCAGATCTGACATTCCTGTGCT
1 GATTTGGCATTCCTGTGTTTACAGAGAACAGATCGAAGACATAGCAGATCTGACATTCCTGTGCT
* * *
58154908 TACAGCGAGGCAGATCAAAGATTTTAACATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAG-A
66 TACAGCGAAGCAGATCAAAGATTTCAACATGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGAA
58154972 TAGCA
131 TAGCA
* * *
58154977 TATTTGGCATCCCTGTGTTTACAGAGAACAGATCGAAGACATAGCAGATCTGATATTCCTGTGCT
1 GATTTGGCATTCCTGTGTTTACAGAGAACAGATCGAAGACATAGCAGATCTGACATTCCTGTGCT
* *
58155042 TACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAAC-AGATCGAAGA
66 TACAGCGAAGCAGATCAAAGATTTCAACATGGCATCCCTGTGTTTATAGGGAACAAG-TCGAAGA
58155106 CATAGCA
130 -ATAGCA
* * * * *
58155113 GATCTGACATTCCTGTGCTTACAGCGAAGCAGATTGAAGA
1 GATTTGGCATTCCTGTGTTTACAGAGAA-CAGATCGAAGA
58155153 TTTCAGTATG
Statistics
Matches: 153, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
133 2 0.01
134 113 0.74
136 28 0.18
137 10 0.07
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (135 bp):
GATTTGGCATTCCTGTGTTTACAGAGAACAGATCGAAGACATAGCAGATCTGACATTCCTGTGCT
TACAGCGAAGCAGATCAAAGATTTCAACATGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGAA
TAGCA
Found at i:58155195 original size:90 final size:90
Alignment explanation
Indices: 58154981--58155186 Score: 367
Period size: 90 Copynumber: 2.3 Consensus size: 90
58154971 ATAGCATATT
* * *
58154981 TGGCATCCCTGTGTTTACAGAGAACAGATCGAAGACATAGCAGATCTGATATTCCTGTGCTTACA
1 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGACATAGCAGATCTGACATTCCTGTGCTTACA
58155046 GCGAAGCAGATCGAAGATTTCAGCA
66 GCGAAGCAGATCGAAGATTTCAGCA
58155071 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGACATAGCAGATCTGACATTCCTGTGCTTACA
1 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGACATAGCAGATCTGACATTCCTGTGCTTACA
* *
58155136 GCGAAGCAGATTGAAGATTTCAGTA
66 GCGAAGCAGATCGAAGATTTCAGCA
58155161 TGGCATCCCTGTGTTTATAGGGAACA
1 TGGCATCCCTGTGTTTATAGGGAACA
58155187 AGTTGAAGAA
Statistics
Matches: 111, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 111 1.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (90 bp):
TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGACATAGCAGATCTGACATTCCTGTGCTTACA
GCGAAGCAGATCGAAGATTTCAGCA
Found at i:58155669 original size:19 final size:19
Alignment explanation
Indices: 58155645--58155718 Score: 132
Period size: 19 Copynumber: 3.9 Consensus size: 19
58155635 ATAATCTTCA
58155645 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
58155664 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
58155683 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
58155701 ATGAAATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
58155719 AGATATGATT
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
18 17 0.32
19 36 0.68
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:58155693 original size:37 final size:38
Alignment explanation
Indices: 58155645--58155725 Score: 132
Period size: 37 Copynumber: 2.2 Consensus size: 38
58155635 ATAATCTTCA
*
58155645 ATGATATGCAATCTTAGATATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGATATGAAATGCAATCTTAGAT
58155683 ATGAT-TGCAATCTTAGATATGAAATGCAATCTTAGA-
1 ATGATATGCAATCTTAGATATGAAATGCAATCTTAGAT
58155719 A-GATATG
1 ATGATATG
58155726 ATTTTGTAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
35 3 0.07
36 3 0.07
37 30 0.73
38 5 0.12
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (38 bp):
ATGATATGCAATCTTAGATATGAAATGCAATCTTAGAT
Found at i:58157669 original size:8 final size:9
Alignment explanation
Indices: 58157631--58157671 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
58157621 TTTTAAATTT
58157631 TTTTTGAAT-
1 TTTTT-AATA
58157640 TTTTTATATA
1 TTTTTA-ATA
58157650 TTTTTAATA
1 TTTTTAATA
58157659 TTTTTAA-A
1 TTTTTAATA
58157667 TTTTT
1 TTTTT
58157672 TGTTGATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 7 0.23
9 17 0.57
10 6 0.20
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (9 bp):
TTTTTAATA
Found at i:58160428 original size:18 final size:18
Alignment explanation
Indices: 58160407--58160449 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
58160397 AAATTGGAAA
58160407 GATAAA-AAAAATAAAGAT
1 GATAAATAAAAA-AAAGAT
*
58160425 GATAAATAATAAAAAGAT
1 GATAAATAAAAAAAAGAT
58160443 GA-AAATA
1 GATAAATA
58160450 TCATCATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 5 0.22
18 14 0.61
19 4 0.17
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.19
Consensus pattern (18 bp):
GATAAATAAAAAAAAGAT
Found at i:58163970 original size:18 final size:18
Alignment explanation
Indices: 58163939--58163974 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
58163929 GAAATTAAAC
58163939 TTAAGTTGAAAAAATAAT
1 TTAAGTTGAAAAAATAAT
58163957 TTAA-TTGAATAAAATAAT
1 TTAAGTTGAA-AAAATAAT
58163975 ATTTTGATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (18 bp):
TTAAGTTGAAAAAATAAT
Found at i:58169005 original size:6 final size:6
Alignment explanation
Indices: 58168990--58169029 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
58168980 ATAATTTAAT
58168990 AAAT-A AAATAA AAATATA AAATTAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATA-A AAA-TAA AAATAA AAATAA AAA
58169030 ACATATAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 4 0.12
6 18 0.56
7 8 0.25
8 2 0.06
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
AAATAA
Found at i:58169010 original size:13 final size:13
Alignment explanation
Indices: 58168992--58169029 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
58168982 AATTTAATAA
58168992 ATAAAATAAAAAT
1 ATAAAATAAAAAT
58169005 ATAAAATTAAAAAT
1 ATAAAA-TAAAAAT
58169019 A-AAAATAAAAA
1 ATAAAATAAAAA
58169030 ACATATAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 6 0.25
13 10 0.42
14 8 0.33
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
ATAAAATAAAAAT
Found at i:58169022 original size:12 final size:12
Alignment explanation
Indices: 58168970--58169029 Score: 59
Period size: 12 Copynumber: 4.9 Consensus size: 12
58168960 CCCAATCATA
*
58168970 AAAATTACAAAT
1 AAAATTAAAAAT
*
58168982 -AATTTAATAAAT
1 AAAATTAA-AAAT
*
58168994 AAAATAAAAATAT
1 AAAATTAAAA-AT
58169007 AAAATTAAAAAT
1 AAAATTAAAAAT
*
58169019 AAAAATAAAAA
1 AAAATTAAAAA
58169030 ACATATAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
11 5 0.13
12 18 0.46
13 16 0.41
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (12 bp):
AAAATTAAAAAT
Found at i:58169063 original size:9 final size:9
Alignment explanation
Indices: 58169049--58169108 Score: 66
Period size: 9 Copynumber: 6.7 Consensus size: 9
58169039 TTTATACAAA
58169049 TAATTTGGT
1 TAATTTGGT
*
58169058 TAATTTGGG
1 TAATTTGGT
* *
58169067 TAATTCGGG
1 TAATTTGGT
*
58169076 TAATTCGGT
1 TAATTTGGT
* *
58169085 TAATTCGAT
1 TAATTTGGT
58169094 TAATTTGGT
1 TAATTTGGT
58169103 TAATTT
1 TAATTT
58169109 TATACTTATT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 45 1.00
ACGTcount: A:0.25, C:0.05, G:0.22, T:0.48
Consensus pattern (9 bp):
TAATTTGGT
Found at i:58170384 original size:16 final size:16
Alignment explanation
Indices: 58170340--58170385 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
58170330 TATGCTATTT
*
58170340 TTTTAT-TTTTATATTA
1 TTTTATATTTTA-AATA
*
58170356 TTTTAAATTTTAAATA
1 TTTTATATTTTAAATA
58170372 TTTTATATTTTAAA
1 TTTTATATTTTAAA
58170386 ATTATTTACT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 21 0.81
17 5 0.19
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTATATTTTAAATA
Found at i:58170393 original size:17 final size:17
Alignment explanation
Indices: 58170346--58170392 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
58170336 ATTTTTTTAT
*
58170346 TTTTATATTATTTTAAA
1 TTTTAAATTATTTTAAA
*
58170363 TTTTAAA-TATTTTATA
1 TTTTAAATTATTTTAAA
58170379 TTTTAAAATTATTT
1 TTTT-AAATTATTT
58170393 ACTAACGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 12 0.46
17 9 0.35
18 5 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTAAATTATTTTAAA
Found at i:58177909 original size:6 final size:6
Alignment explanation
Indices: 58177893--58177936 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
58177883 ACAATGTTGG
* * *
58177893 AAATGA TAATGA CAATGA CAATGA AAATGA AAATGA AAATGA AA
1 AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA AA
58177937 GGTGCAGTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.61, C:0.05, G:0.16, T:0.18
Consensus pattern (6 bp):
AAATGA
Found at i:58193231 original size:17 final size:18
Alignment explanation
Indices: 58193201--58193234 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
58193191 GATATGAGGA
58193201 AATTGAGAAATGATGATG
1 AATTGAGAAATGATGATG
58193219 AATTGAG-AATGATGAT
1 AATTGAGAAATGATGAT
58193235 ATGTGAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.44, C:0.00, G:0.26, T:0.29
Consensus pattern (18 bp):
AATTGAGAAATGATGATG
Found at i:58195286 original size:6 final size:6
Alignment explanation
Indices: 58195263--58195315 Score: 63
Period size: 6 Copynumber: 8.8 Consensus size: 6
58195253 GCAAATGGAT
* * *
58195263 CATTTCC CATTTT TATTTT CATTT- CATTTC CATTTC CATTTC CATTTC
1 CATTT-C CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC
58195311 CATTT
1 CATTT
58195316 TTGAGAAACA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
5 5 0.12
6 32 0.76
7 5 0.12
ACGTcount: A:0.17, C:0.26, G:0.00, T:0.57
Consensus pattern (6 bp):
CATTTC
Found at i:58198024 original size:20 final size:22
Alignment explanation
Indices: 58197985--58198035 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
58197975 AAAAGTAATG
58197985 AAAATT-TATTTTCTTAGAA-T
1 AAAATTCTATTTTCTTAGAATT
58198005 -AAATTCTATTTTC-TAGGAATT
1 AAAATTCTATTTTCTTA-GAATT
58198026 AAAATTCTAT
1 AAAATTCTAT
58198036 CGGTTTCTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 7 0.26
20 10 0.37
21 1 0.04
22 9 0.33
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (22 bp):
AAAATTCTATTTTCTTAGAATT
Found at i:58201613 original size:49 final size:49
Alignment explanation
Indices: 58201553--58201793 Score: 401
Period size: 49 Copynumber: 4.9 Consensus size: 49
58201543 TATTAAAATT
58201553 TGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAA
1 TGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAA
*
58201602 TGTGAAGGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAA
1 TGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAA
*
58201651 TGTGAAGGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAA
1 TGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAA
* *
58201700 TGTGAAAGTGTATATATATGTGATAAGGCCTCATGGCCGATGTGGTGAA
1 TGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAA
* * * * *
58201749 TGTGAAAGTGTATGTATATGTGGTAAAGCCGAATGGCCAATGTGA
1 TGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGA
58201794 ATGTTGTAAC
Statistics
Matches: 181, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 181 1.00
ACGTcount: A:0.31, C:0.09, G:0.30, T:0.30
Consensus pattern (49 bp):
TGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAA
Found at i:58201897 original size:37 final size:37
Alignment explanation
Indices: 58201847--58201998 Score: 286
Period size: 37 Copynumber: 4.1 Consensus size: 37
58201837 GTTCCGAGTG
58201847 AGACCCGATGACTACGTGTGGAGATTATGACCGGGTA
1 AGACCCGATGACTACGTGTGGAGATTATGACCGGGTA
58201884 AGACCCGATGACTACGTGTGGAGATTATGACCGGGTA
1 AGACCCGATGACTACGTGTGGAGATTATGACCGGGTA
58201921 AGACCCGATGACTACGTGTGGAGATTATGACCGGGTA
1 AGACCCGATGACTACGTGTGGAGATTATGACCGGGTA
* *
58201958 AGACCCGATGACTACGTGTGGAGGTTATGTCCGGGTA
1 AGACCCGATGACTACGTGTGGAGATTATGACCGGGTA
58201995 AGAC
1 AGAC
58201999 TTCGTAATAA
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 113 1.00
ACGTcount: A:0.26, C:0.19, G:0.33, T:0.22
Consensus pattern (37 bp):
AGACCCGATGACTACGTGTGGAGATTATGACCGGGTA
Found at i:58203858 original size:40 final size:40
Alignment explanation
Indices: 58203802--58203952 Score: 257
Period size: 40 Copynumber: 3.8 Consensus size: 40
58203792 GAGAATTGAG
* *
58203802 AGTGATGCATCTGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
58203842 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
58203882 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
* * *
58203922 AGTGATGTATCCGGGCTAGGTCCCGAAGAGC
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGC
58203953 GATCATGCTG
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 106 1.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
Found at i:58204795 original size:40 final size:41
Alignment explanation
Indices: 58204697--58204795 Score: 114
Period size: 41 Copynumber: 2.4 Consensus size: 41
58204687 TTCGAATGGT
* ** * *
58204697 ATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTTACTAA
1 ATCCGGGCTATGTCCCGAAGGCAATTGTGCGAAGTCACTAA
58204738 ATCCGGGCTAAT-TCCCGAAGGCAATTGTGCGAA-TCACTATA
1 ATCCGGGCT-ATGTCCCGAAGGCAATTGTGCGAAGTCACTA-A
58204779 A-CCGGGCTATGTCCCGA
1 ATCCGGGCTATGTCCCGA
58204796 GGACAATCGA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
39 2 0.04
40 18 0.36
41 29 0.58
42 1 0.02
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.25
Consensus pattern (41 bp):
ATCCGGGCTATGTCCCGAAGGCAATTGTGCGAAGTCACTAA
Found at i:58204818 original size:40 final size:40
Alignment explanation
Indices: 58204740--58204837 Score: 94
Period size: 40 Copynumber: 2.5 Consensus size: 40
58204730 GTTACTAAAT
* *
58204740 CCGGGCTAATTCCCGAAGGCAATTGTGCGAATCACTATAA
1 CCGGGCTAATTCCCGAAGGCAATCGAGCGAATCACTATAA
* * *
58204780 CCGGGCT-ATGTCCCG-AGGACAATCGAGCGAGTCGCTATAT
1 CCGGGCTAAT-TCCCGAAGG-CAATCGAGCGAATCACTATAA
* *
58204820 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAATTCCCGAAGG
58204838 TACGTGATTC
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
39 13 0.28
40 34 0.72
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (40 bp):
CCGGGCTAATTCCCGAAGGCAATCGAGCGAATCACTATAA
Found at i:58207854 original size:49 final size:48
Alignment explanation
Indices: 58207794--58207942 Score: 271
Period size: 49 Copynumber: 3.0 Consensus size: 48
58207784 TATTAAAATT
58207794 TGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAA
1 TGTG-AAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAA
58207843 TGTGAAGGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAA
1 TGTGAA-GTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAA
58207892 TGTGATAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAA
1 TGTGA-AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAA
58207941 TG
1 TG
58207943 GCCGATGTGA
Statistics
Matches: 98, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
48 2 0.02
49 95 0.97
50 1 0.01
ACGTcount: A:0.31, C:0.08, G:0.30, T:0.32
Consensus pattern (48 bp):
TGTGAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAA
Found at i:58207944 original size:16 final size:16
Alignment explanation
Indices: 58207923--58207958 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
58207913 GATAAGGCCT
58207923 AATGGCCGATGTGATG
1 AATGGCCGATGTGATG
58207939 AATGGCCGATGTGATG
1 AATGGCCGATGTGATG
58207955 AATG
1 AATG
58207959 TGAAGGTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.11, G:0.36, T:0.25
Consensus pattern (16 bp):
AATGGCCGATGTGATG
Found at i:58207954 original size:65 final size:65
Alignment explanation
Indices: 58207874--58208007 Score: 252
Period size: 65 Copynumber: 2.1 Consensus size: 65
58207864 GATAAGGCCT
58207874 AATGGCCGATGTGATGAATGTGATA-GTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 AATGGCCGATGTGATGAATGTGA-AGGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
58207938 G
65 G
58207939 AATGGCCGATGTGATGAATGTGAAGGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGGCCGATGTGATGAATGTGAAGGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
58208004 AATG
1 AATG
58208008 TGAAAGTGTA
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
64 1 0.01
65 67 0.99
ACGTcount: A:0.30, C:0.09, G:0.31, T:0.30
Consensus pattern (65 bp):
AATGGCCGATGTGATGAATGTGAAGGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:58207995 original size:49 final size:49
Alignment explanation
Indices: 58207939--58208099 Score: 250
Period size: 49 Copynumber: 3.3 Consensus size: 49
58207929 CGATGTGATG
*
58207939 AATGGCCGATGTGATGAATGTGAAGGTGTATATATATGTGATAAGGCCT
1 AATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCT
58207988 AATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCT
1 AATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCT
* * * * * *
58208037 CATGGCCGATGTGGTGAATGTGAAAGTGTATGTATATGTGGTAAAGCCG
1 AATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCT
*
58208086 AATGGCCAATGTGA
1 AATGGCCGATGTGA
58208100 ATGTTGTAAC
Statistics
Matches: 102, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 102 1.00
ACGTcount: A:0.30, C:0.09, G:0.31, T:0.29
Consensus pattern (49 bp):
AATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCT
Found at i:58208023 original size:114 final size:114
Alignment explanation
Indices: 58207825--58208056 Score: 437
Period size: 114 Copynumber: 2.0 Consensus size: 114
58207815 GATAAGGCCT
58207825 AATGGCCGATGTGATGAATGTGAAGGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGGCCGATGTGATGAATGTGAAGGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
58207890 AATGTGATAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
66 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
58207939 AATGGCCGATGTGATGAATGTGAAGGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGGCCGATGTGATGAATGTGAAGGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
58208004 AATGTGAAAGTGTATATATATGTGATAAGGCCTCATGGCCGATGTGGTG
66 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
58208053 AATG
1 AATG
58208057 TGAAAGTGTA
Statistics
Matches: 115, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 115 1.00
ACGTcount: A:0.30, C:0.09, G:0.31, T:0.30
Consensus pattern (114 bp):
AATGGCCGATGTGATGAATGTGAAGGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:58208057 original size:163 final size:163
Alignment explanation
Indices: 58207794--58208099 Score: 522
Period size: 163 Copynumber: 1.9 Consensus size: 163
58207784 TATTAAAATT
*
58207794 TGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAGGTGTATATA
1 TGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* * *
58207859 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGATAGTGTATATATATGTGATAAGGCCTA
66 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAAGCCGA
*
58207924 ATGGCCGATGTGATGAATGGCCGATGTGATGAA
131 ATGGCCAATGTGATGAATGGCCGATGTGATGAA
*
58207957 TGTGAAGGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* * * *
58208022 TATGTGATAAGGCCTCATGGCCGATGTGGTGAATGTGAAAGTGTATGTATATGTGGTAAAGCCGA
66 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAAGCCGA
58208087 ATGGCCAATGTGA
131 ATGGCCAATGTGA
58208100 ATGTTGTAAC
Statistics
Matches: 133, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
163 133 1.00
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.30
Consensus pattern (163 bp):
TGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAAGCCGA
ATGGCCAATGTGATGAATGGCCGATGTGATGAA
Found at i:58208196 original size:37 final size:37
Alignment explanation
Indices: 58208146--58208267 Score: 217
Period size: 37 Copynumber: 3.3 Consensus size: 37
58208136 GAAATATGTT
*
58208146 CCGGGTGAGACCCGATGACTACGTGTGGAGATTATGA
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
58208183 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
* *
58208220 CCGGGTAAGACCCGATGACTACGTGTGGAGGTTATGT
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
58208257 CCGGGTAAGAC
1 CCGGGTAAGAC
58208268 TTCGTAATAA
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 82 1.00
ACGTcount: A:0.25, C:0.20, G:0.34, T:0.21
Consensus pattern (37 bp):
CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
Done.