Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D03
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: 50986338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 218898 characters in sequence are not A, C, G, or T
File 133 of 170
Found at i:40415151 original size:20 final size:20
Alignment explanation
Indices: 40415033--40415159 Score: 89
Period size: 20 Copynumber: 6.3 Consensus size: 20
40415023 AATGAAGAAG
* * *
40415033 TGCCCCTGTTTGTACTTCGG
1 TGCCCCTGATTGCACTTCGA
* * **
40415053 TACCCCTGAATGCACATT-TT
1 TGCCCCTGATTGCAC-TTCGA
*
40415073 TGCCCCTGTTTGCACTTCGA
1 TGCCCCTGATTGCACTTCGA
*
40415093 TGCCCCTGAATGCACATAT-G-
1 TGCCCCTGATTGCAC-T-TCGA
* * *
40415113 TGCCCCTAATTACATTTCGA
1 TGCCCCTGATTGCACTTCGA
*
40415133 TGCCCCTGATTGCACTTCGG
1 TGCCCCTGATTGCACTTCGA
40415153 TGCCCCT
1 TGCCCCT
40415160 ATTATACATC
Statistics
Matches: 80, Mismatches: 21, Indels: 12
0.71 0.19 0.11
Matches are distributed among these distances:
18 1 0.01
19 4 0.05
20 70 0.88
21 4 0.05
22 1 0.01
ACGTcount: A:0.16, C:0.33, G:0.18, T:0.33
Consensus pattern (20 bp):
TGCCCCTGATTGCACTTCGA
Found at i:40415156 original size:40 final size:42
Alignment explanation
Indices: 40415087--40415182 Score: 117
Period size: 40 Copynumber: 2.3 Consensus size: 42
40415077 CCTGTTTGCA
*
40415087 CTTCGATGCCCCTGAATGCACATATGTGCCCCTAAT-TACAT
1 CTTCGATGCCCCTGAATGCACATAGGTGCCCCTAATATACAT
* * * *
40415128 -TTCGATGCCCCTGATTGCACTTCGGTGCCCCTATTATACAT
1 CTTCGATGCCCCTGAATGCACATAGGTGCCCCTAATATACAT
40415169 CTAT-GATGCCCCTG
1 CT-TCGATGCCCCTG
40415183 GTGTGGTGTA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
40 30 0.64
41 5 0.11
42 11 0.23
43 1 0.02
ACGTcount: A:0.20, C:0.32, G:0.17, T:0.31
Consensus pattern (42 bp):
CTTCGATGCCCCTGAATGCACATAGGTGCCCCTAATATACAT
Found at i:40420025 original size:134 final size:134
Alignment explanation
Indices: 40419782--40420101 Score: 374
Period size: 134 Copynumber: 2.4 Consensus size: 134
40419772 ATAAGCTGTA
* * * * ** *
40419782 ATGGGGTATACTGTGTAAGACCATAGCTCAGCTATGGCAGCAGAGAGAGTTTGTTAGAACATTAA
1 ATGGGGTATAATGTGTAAGACCATAGCTCAGCTATGGCAACATAGAAAGTCCGCTAGAACATTAA
* * * *
40419847 ACATGGGGTATAATGTGTAAGACCATAGCTATGCTACGATAACATAGCGAATCCACCAGAACATT
66 ACATGGGGTATAAAGTGTAAGACCATAGCTACGCTACGACAACATAGAGAATCCACCAGAACATT
40419912 AAAC
131 AAAC
* * *
40419916 ATGGGGTATAATGCGTAAGACCATAGCTCGGCTATGGCAACATAGAAAGTCCGCTAGGACATTAA
1 ATGGGGTATAATGTGTAAGACCATAGCTCAGCTATGGCAACATAGAAAGTCCGCTAGAACATTAA
* * * * ** *
40419981 ATATGGGGTATAAAGTGTAAGACCATAGCT-CGACTATGACAACATAGATAGTCTTCCAGGACAT
66 ACATGGGGTATAAAGTGTAAGACCATAGCTACG-CTACGACAACATAGAGAATCCACCAGAACAT
40420045 TAAAC
130 TAAAC
* * * * *
40420050 ATGGGGTATGATGTGTAAAACCATAACTTAG-TGATGGCAACATATAAAGTCC
1 ATGGGGTATAATGTGTAAGACCATAGCTCAGCT-ATGGCAACATAGAAAGTCC
40420102 ATTGGGACAA
Statistics
Matches: 156, Mismatches: 28, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
133 2 0.01
134 154 0.99
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (134 bp):
ATGGGGTATAATGTGTAAGACCATAGCTCAGCTATGGCAACATAGAAAGTCCGCTAGAACATTAA
ACATGGGGTATAAAGTGTAAGACCATAGCTACGCTACGACAACATAGAGAATCCACCAGAACATT
AAAC
Found at i:40420091 original size:67 final size:66
Alignment explanation
Indices: 40419782--40420101 Score: 293
Period size: 67 Copynumber: 4.8 Consensus size: 66
40419772 ATAAGCTGTA
* * * * ** ** *
40419782 ATGGGGTATACTGTGTAAGACCATAGCTCAGCTATGGCAGCAGAGAGAGTTTGTTAGAACATTAA
1 ATGGGGTATAATGTGTAAGACCATAGCTCAG-TATGGCAACATAGAAAGTCCGCCAGGACATTAA
40419847 AC
65 AC
* ** * * *
40419849 ATGGGGTATAATGTGTAAGACCATAGCT-ATGCTACGATAACATAGCGAA-TCCACCAGAACATT
1 ATGGGGTATAATGTGTAAGACCATAGCTCA-G-TATGGCAACATAG-AAAGTCCGCCAGGACATT
40419912 AAAC
63 AAAC
* * *
40419916 ATGGGGTATAATGCGTAAGACCATAGCTCGGCTATGGCAACATAGAAAGTCCGCTAGGACATTAA
1 ATGGGGTATAATGTGTAAGACCATAGCTCAG-TATGGCAACATAGAAAGTCCGCCAGGACATTAA
*
40419981 AT
65 AC
* * * * **
40419983 ATGGGGTATAAAGTGTAAGACCATAGCTCGACTATGACAACATAGATAGTCTTCCAGGACATTAA
1 ATGGGGTATAATGTGTAAGACCATAGCTC-AGTATGGCAACATAGAAAGTCCGCCAGGACATTAA
40420048 AC
65 AC
* * * * *
40420050 ATGGGGTATGATGTGTAAAACCATAACTTAGTGATGGCAACATATAAAGTCC
1 ATGGGGTATAATGTGTAAGACCATAGCTCAGT-ATGGCAACATAGAAAGTCC
40420102 ATTGGGACAA
Statistics
Matches: 204, Mismatches: 43, Indels: 12
0.79 0.17 0.05
Matches are distributed among these distances:
66 5 0.02
67 198 0.97
68 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (66 bp):
ATGGGGTATAATGTGTAAGACCATAGCTCAGTATGGCAACATAGAAAGTCCGCCAGGACATTAAA
C
Found at i:40423782 original size:62 final size:60
Alignment explanation
Indices: 40423671--40423788 Score: 166
Period size: 62 Copynumber: 1.9 Consensus size: 60
40423661 ATCACTTTAA
* * * *
40423671 TATTAAATTTAATCTAATATTTATGAAGATAAATATTTAATTTAATTTAATATTAAATCT
1 TATTAAATTTAATATAATATTTATGAAGATAAACATTAAATTGAATTTAATATTAAATCT
40423731 TATTAAA-TTAATATAATATTTATCGACAAGATAAACATTAAATTGAATTTAATATTAA
1 TATTAAATTTAATATAATATTTAT-G--AAGATAAACATTAAATTGAATTTAATATTAA
40423789 GATAATCACT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
59 15 0.29
60 8 0.16
62 28 0.55
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (60 bp):
TATTAAATTTAATATAATATTTATGAAGATAAACATTAAATTGAATTTAATATTAAATCT
Found at i:40426737 original size:11 final size:11
Alignment explanation
Indices: 40426721--40426747 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
40426711 CTGATAAATA
40426721 AGCCTATTTAT
1 AGCCTATTTAT
40426732 AGCCTATTTAT
1 AGCCTATTTAT
40426743 AGCCT
1 AGCCT
40426748 TCAAGTGGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.41
Consensus pattern (11 bp):
AGCCTATTTAT
Found at i:40436999 original size:159 final size:159
Alignment explanation
Indices: 40436704--40437021 Score: 600
Period size: 159 Copynumber: 2.0 Consensus size: 159
40436694 TGGTTGCATG
40436704 AGTATAACATAAAAATGATAACAAGTCCAACTCCTGAAGAATTCCGAGGGAAAACAAAATATTTC
1 AGTATAACATAAAAATGATAACAAGTCCAACTCCTGAAGAATTCCGAGGGAAAACAAAATATTTC
*
40436769 AAGTCCTTGGACCGAGTAAAATTTGTTCTACAGACAAACTAGATAACATGGTTAAAACAGTAGTC
66 AAGTCCTTGGACCGAGTAAAATTTGTTCTACAGACAAACTAGATAACATGGTTAAAACAGTAATC
*
40436834 TGTGTTCCTGTTGTTTACATCTGCCTAAC
131 TCTGTTCCTGTTGTTTACATCTGCCTAAC
*
40436863 AGTATAACATAAAAATGATAACAAGTCCAACTCCTGAAGAATTCTGAGGGAAAACAAAATATTTC
1 AGTATAACATAAAAATGATAACAAGTCCAACTCCTGAAGAATTCCGAGGGAAAACAAAATATTTC
*
40436928 AAGTCCTTGGACCGAGTAAAATTTGTTCTACAGACAAATTAGATAACATGGTTAAAACAGTAATC
66 AAGTCCTTGGACCGAGTAAAATTTGTTCTACAGACAAACTAGATAACATGGTTAAAACAGTAATC
40436993 TCTGTTCCTGTTGTTTACATCTGCCTAAC
131 TCTGTTCCTGTTGTTTACATCTGCCTAAC
40437022 TTACCCAACC
Statistics
Matches: 155, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
159 155 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (159 bp):
AGTATAACATAAAAATGATAACAAGTCCAACTCCTGAAGAATTCCGAGGGAAAACAAAATATTTC
AAGTCCTTGGACCGAGTAAAATTTGTTCTACAGACAAACTAGATAACATGGTTAAAACAGTAATC
TCTGTTCCTGTTGTTTACATCTGCCTAAC
Found at i:40437281 original size:21 final size:21
Alignment explanation
Indices: 40437248--40437291 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
40437238 CACTCATTTC
* * *
40437248 TTTTTTCAGAATTAATTTTAT
1 TTTTTTAAAAATTAATTTCAT
*
40437269 TTTTTTAAAAATTGATTTCAT
1 TTTTTTAAAAATTAATTTCAT
40437290 TT
1 TT
40437292 ACGAAAAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.61
Consensus pattern (21 bp):
TTTTTTAAAAATTAATTTCAT
Found at i:40437529 original size:22 final size:22
Alignment explanation
Indices: 40437495--40437536 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
40437485 AATTGTTCTA
40437495 TAAAAATCTAAATAATTCCATG
1 TAAAAATCTAAATAATTCCATG
*
40437517 TAAAACATC-AAATTATTCCA
1 TAAAA-ATCTAAATAATTCCA
40437537 CAAAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.50, C:0.17, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAAAATCTAAATAATTCCATG
Found at i:40452993 original size:18 final size:19
Alignment explanation
Indices: 40452967--40453003 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
40452957 ATTGAAATAG
*
40452967 TTATTATTATTTT-GATTC
1 TTATAATTATTTTAGATTC
40452985 TTATAATTATTTTAGATTC
1 TTATAATTATTTTAGATTC
40453004 ACATGTTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.62
Consensus pattern (19 bp):
TTATAATTATTTTAGATTC
Found at i:40454504 original size:43 final size:43
Alignment explanation
Indices: 40454445--40454669 Score: 204
Period size: 43 Copynumber: 5.3 Consensus size: 43
40454435 CTTTAGAAAT
* * * *
40454445 AAACGCCGCTAAAGGTCATGACCTTTAGCGGCGCTTTTCCCAT
1 AAACGCCGCTATAGGTCATCACTTTTAGCGGCGCTTTTCCCAC
*
40454488 AAATGCCGCTATAGGTCATCACTTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGGTCATCACTTTTAGCGGCGCTTTTCCCAC
* * * * *
40454531 AAACGCTGCTATAGATCATCACTTTTAGCAGCGTTTTTTCCAC
1 AAACGCCGCTATAGGTCATCACTTTTAGCGGCGCTTTTCCCAC
*** * * **
40454574 AAACGCCGCTATAAAACA-GA-TCTTTAGCGACGCTTTTTCGTAC
1 AAACGCCGCTATAGGTCATCACT-TTTAGCGGCGC-TTTTCCCAC
* * * * * *
40454617 AAACGCCGCTATAGGACA-AACCTTTAGCTGCACTTTTCACAC
1 AAACGCCGCTATAGGTCATCACTTTTAGCGGCGCTTTTCCCAC
40454659 AAACGCCGCTA
1 AAACGCCGCTA
40454670 AAGGCATATC
Statistics
Matches: 149, Mismatches: 30, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
41 1 0.01
42 27 0.18
43 121 0.81
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.28
Consensus pattern (43 bp):
AAACGCCGCTATAGGTCATCACTTTTAGCGGCGCTTTTCCCAC
Found at i:40454939 original size:43 final size:43
Alignment explanation
Indices: 40454862--40454945 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 43
40454852 ACATATGCAA
* * ** *
40454862 GGTAATAAAACATACAATGCATTTTCTTGGTCAAGTAAATCTT
1 GGTAATAAAACATACAATACATTTACTTAATCAAGGAAATCTT
* *
40454905 GGTAATAAAAGATATAATACATTTACTTAATCAAGGAAATC
1 GGTAATAAAACATACAATACATTTACTTAATCAAGGAAATC
40454946 GTGTAATGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (43 bp):
GGTAATAAAACATACAATACATTTACTTAATCAAGGAAATCTT
Found at i:40458079 original size:21 final size:22
Alignment explanation
Indices: 40458053--40458103 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 22
40458043 TTTCAAGGCA
*
40458053 GAAAATTAGGGATTTTAGGG-G
1 GAAAATTAGGGATATTAGGGAG
*
40458074 GAAAATTGGGGATATTAGGGAG
1 GAAAATTAGGGATATTAGGGAG
40458096 GAAAATTA
1 GAAAATTA
40458104 TAAAATGGCG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 18 0.69
22 8 0.31
ACGTcount: A:0.39, C:0.00, G:0.35, T:0.25
Consensus pattern (22 bp):
GAAAATTAGGGATATTAGGGAG
Found at i:40458745 original size:15 final size:15
Alignment explanation
Indices: 40458725--40458753 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40458715 AAACCATAAT
40458725 CCATAATCCCTAAAA
1 CCATAATCCCTAAAA
40458740 CCATAATCCCTAAA
1 CCATAATCCCTAAA
40458754 CTTTAAAATA
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:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (15 bp):
CCATAATCCCTAAAA
Found at i:40458761 original size:22 final size:22
Alignment explanation
Indices: 40458711--40458754 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
40458701 AATAGTAACT
*
40458711 CCTAAAACCATAATCCATAATC
1 CCTAAAACCATAATCCATAAAC
*
40458733 CCTAAAACCATAATCCCTAAAC
1 CCTAAAACCATAATCCATAAAC
40458755 TTTAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.20
Consensus pattern (22 bp):
CCTAAAACCATAATCCATAAAC
Found at i:40459099 original size:21 final size:21
Alignment explanation
Indices: 40459075--40459155 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
40459065 TCTAACCCCT
*
40459075 AACCCCTAAACCTTAAATCTC
1 AACCCATAAACCTTAAATCTC
* *
40459096 AACCCTTAAACCAT-AATCTC
1 AACCCATAAACCTTAAATCTC
* * *
40459116 TAATCCATAATCCCTAAATC-C
1 -AACCCATAAACCTTAAATCTC
40459137 ATACTCCATAAACCTTAAA
1 A-AC-CCATAAACCTTAAA
40459156 ATATGAACTC
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
20 7 0.15
21 24 0.51
22 16 0.34
ACGTcount: A:0.41, C:0.33, G:0.00, T:0.26
Consensus pattern (21 bp):
AACCCATAAACCTTAAATCTC
Found at i:40459137 original size:15 final size:15
Alignment explanation
Indices: 40459102--40459139 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
40459092 TCTCAACCCT
*
40459102 TAAA-CCATAATCTC
1 TAAATCCATAATCCC
40459116 T-AATCCATAATCCC
1 TAAATCCATAATCCC
40459130 TAAATCCATA
1 TAAATCCATA
40459140 CTCCATAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 11 0.52
15 8 0.38
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:40459155 original size:22 final size:23
Alignment explanation
Indices: 40459081--40459155 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 23
40459071 CCCTAACCCC
*
40459081 TAAACCTTAAATCTCA-AC-CCT
1 TAAACCTTAAATCTCATACTCCA
* *
40459102 TAAACCAT-AATCTC-TAATCCA
1 TAAACCTTAAATCTCATACTCCA
* *
40459123 TAATCCCTAAATC-CATACTCCA
1 TAAACCTTAAATCTCATACTCCA
40459145 TAAACCTTAAA
1 TAAACCTTAAA
40459156 ATATGAACTC
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
20 7 0.17
21 16 0.38
22 19 0.45
ACGTcount: A:0.41, C:0.31, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAACCTTAAATCTCATACTCCA
Found at i:40459267 original size:295 final size:296
Alignment explanation
Indices: 40458927--40459516 Score: 888
Period size: 295 Copynumber: 2.0 Consensus size: 296
40458917 CAATATATTT
*
40458927 AATTTATTATTATCTCTTTTATAATTATATAAGAACATATTTAAAATATAAATTAAAAAAATAAT
1 AATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATT-AAAAAATAAT
* * * *
40458992 TAATCTAAACCCAAAACCCTAACCCGACCCTTGAATCCCTAAAC-CTTAAATCCCTAGT-TCTTA
65 TAATCTAAACCCAAAACCCTAACCCGACCCCTAAATCCCT-AACTCTT-AACCCCTAATGTC-TA
* * *
40459055 ACCCCT-AACATCT-AACCCCTAACCCCTAAACCTTAAATCTCAACCCTTAAACCATAATCTC-T
127 ACCCCTAAACACCTAAACCCCTAACCCCTAAACCTTAAAACCCAACCCTTAAACCATAATC-CAT
40459117 AATCCATAATCCCTAAATCCATACTCCATAAACCTTAAAATA-TGAACTCCTAAACCGGCCTTAA
191 AATCCATAATCCCTAAATCCATACTCCATAAACCTTAAAATAGT-AACTCCTAAACCGGCCTTAA
* *
40459181 ATCTTAAAT-AATCATATAACCTAAACTAAAAACCCTAAACA
255 ATCTTAAATAAATCATACAACCTAAACCAAAAACCCTAAACA
40459222 AATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAATAATT
1 AATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAATAATT
* * ** *
40459287 AATCTAAATCCAAAACCTTAACTTGACCCCTAAATCTCTAACTCTTAACCCCTAATGTCTAACCC
66 AATCTAAACCCAAAACCCTAACCCGACCCCTAAATCCCTAACTCTTAACCCCTAATGTCTAACCC
* *
40459352 CTAAACCCCTAAACCCCTAACCCTTAAACCTTAAAACCCAACCCTTAAACCATAATCCATAATCC
131 CTAAACACCTAAACCCCTAACCCCTAAACCTTAAAACCCAACCCTTAAACCATAATCCATAATCC
* * *
40459417 ATAATCCCTAAATCTATACTCCCTAAACCTTAAAATAGTAACTCCTAAACTGGCCTTAAATCTTA
196 ATAATCCCTAAATCCATACTCCATAAACCTTAAAATAGTAACTCCTAAACCGGCCTTAAATCTTA
*
40459482 AATAAATCATACACCCTAAACCAAAAACCCTAAAC
261 AATAAATCATACAACCTAAACCAAAAACCCTAAAC
40459517 TATAGTGATA
Statistics
Matches: 267, Mismatches: 21, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
293 19 0.07
294 54 0.20
295 165 0.62
296 29 0.11
ACGTcount: A:0.42, C:0.27, G:0.02, T:0.29
Consensus pattern (296 bp):
AATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAATAATT
AATCTAAACCCAAAACCCTAACCCGACCCCTAAATCCCTAACTCTTAACCCCTAATGTCTAACCC
CTAAACACCTAAACCCCTAACCCCTAAACCTTAAAACCCAACCCTTAAACCATAATCCATAATCC
ATAATCCCTAAATCCATACTCCATAAACCTTAAAATAGTAACTCCTAAACCGGCCTTAAATCTTA
AATAAATCATACAACCTAAACCAAAAACCCTAAACA
Found at i:40459338 original size:22 final size:22
Alignment explanation
Indices: 40459312--40459378 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
40459302 CCTTAACTTG
*
40459312 ACCCCTAAATCTCTAACTCTTA
1 ACCCCTAAATCTCTAACCCTTA
* *
40459334 ACCCCT-AATGTCTAACCCCTAA
1 ACCCCTAAATCTCTAA-CCCTTA
* *
40459356 ACCCCTAAACCCCTAACCCTTA
1 ACCCCTAAATCTCTAACCCTTA
40459378 A
1 A
40459379 ACCTTAAAAC
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
21 8 0.22
22 22 0.61
23 6 0.17
ACGTcount: A:0.33, C:0.42, G:0.01, T:0.24
Consensus pattern (22 bp):
ACCCCTAAATCTCTAACCCTTA
Found at i:40459360 original size:8 final size:8
Alignment explanation
Indices: 40459347--40459381 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
40459337 CCTAATGTCT
40459347 AACCCCTA
1 AACCCCTA
40459355 AACCCCTA
1 AACCCCTA
40459363 AACCCCT-
1 AACCCCTA
*
40459370 AACCCTTA
1 AACCCCTA
40459378 AACC
1 AACC
40459382 TTAAAACCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 6 0.24
8 19 0.76
ACGTcount: A:0.37, C:0.49, G:0.00, T:0.14
Consensus pattern (8 bp):
AACCCCTA
Found at i:40459373 original size:15 final size:16
Alignment explanation
Indices: 40459347--40459381 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
40459337 CCTAATGTCT
40459347 AACCCCTAAACCCCTA
1 AACCCCTAAACCCCTA
*
40459363 AACCCCT-AACCCTTA
1 AACCCCTAAACCCCTA
40459378 AACC
1 AACC
40459382 TTAAAACCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.37, C:0.49, G:0.00, T:0.14
Consensus pattern (16 bp):
AACCCCTAAACCCCTA
Found at i:40459379 original size:23 final size:23
Alignment explanation
Indices: 40459345--40459402 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
40459335 CCCCTAATGT
* *
40459345 CTAACCCCTAAACCCCTAAACCC
1 CTAACCCTTAAACCCCTAAAACC
*
40459368 CTAACCCTTAAA-CCTTAAAACC
1 CTAACCCTTAAACCCCTAAAACC
40459390 C-AACCCTTAAACC
1 CTAACCCTTAAACC
40459403 ATAATCCATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.32
22 10 0.32
23 11 0.35
ACGTcount: A:0.38, C:0.45, G:0.00, T:0.17
Consensus pattern (23 bp):
CTAACCCTTAAACCCCTAAAACC
Found at i:40459396 original size:21 final size:22
Alignment explanation
Indices: 40459345--40459402 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 22
40459335 CCCCTAATGT
* *
40459345 CTAACCCCTAAACCCCTAAACCC
1 CTAACCCTTAAA-CCCTAAAACC
*
40459368 CTAACCCTTAAACCTTAAAACC
1 CTAACCCTTAAACCCTAAAACC
40459390 C-AACCCTTAAACC
1 CTAACCCTTAAACC
40459403 ATAATCCATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 12 0.38
22 9 0.28
23 11 0.34
ACGTcount: A:0.38, C:0.45, G:0.00, T:0.17
Consensus pattern (22 bp):
CTAACCCTTAAACCCTAAAACC
Found at i:40459835 original size:41 final size:41
Alignment explanation
Indices: 40459790--40460112 Score: 371
Period size: 41 Copynumber: 7.9 Consensus size: 41
40459780 TAAAATGTTT
* * * *
40459790 TTAGCGGCTCTTTTTCAAAAACACTGCTAAAACCCTAAGCA
1 TTAGCGGCACTTTTTCAAAAACGCCGCTAAAACCCCAAGCA
* ** * *
40459831 TTAGCGGCACTTTTTAAAAAATACCGCTAAAATCCCGAGCA
1 TTAGCGGCACTTTTTCAAAAACGCCGCTAAAACCCCAAGCA
* * *
40459872 TTAGCGGCGCTTTTTAAAAAACGCCGCTAAAACACCAAGCA
1 TTAGCGGCACTTTTTCAAAAACGCCGCTAAAACCCCAAGCA
* *
40459913 TTAGCGACACTTTTTCAAAAACGCCGCTAAAGCCCCCAA-CA
1 TTAGCGGCACTTTTTCAAAAACGCCGCTAAA-ACCCCAAGCA
*
40459954 TTAGCGGCACATTTTCAAAAACGCCGCTAAAACCCCAAGCA
1 TTAGCGGCACTTTTTCAAAAACGCCGCTAAAACCCCAAGCA
* ** * ** *
40459995 CTAGCGGCGTTTTTTAAAAAATACCGCTAAAACACCGAA-CA
1 TTAGCGGCACTTTTTCAAAAACGCCGCTAAAAC-CCCAAGCA
*
40460036 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCAAGCA
1 TTAGCGGCACTTTTTCAAAAACGCCGCTAAAACCCCAAGCA
* * * *
40460077 TTAGCGGCGCATTTTCAAAAACGCAGCTAAAGCCCC
1 TTAGCGGCACTTTTTCAAAAACGCCGCTAAAACCCC
40460113 GAAAGGTAAG
Statistics
Matches: 240, Mismatches: 38, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
40 10 0.04
41 221 0.92
42 9 0.04
ACGTcount: A:0.35, C:0.29, G:0.15, T:0.21
Consensus pattern (41 bp):
TTAGCGGCACTTTTTCAAAAACGCCGCTAAAACCCCAAGCA
Found at i:40460009 original size:123 final size:123
Alignment explanation
Indices: 40459790--40460112 Score: 434
Period size: 123 Copynumber: 2.6 Consensus size: 123
40459780 TAAAATGTTT
* * * * * * **
40459790 TTAGCGGCTCTTTTTCAAAAACACTGCTAAAACCCTAAGCATTAGCGGCACTTTTTAAAAAATAC
1 TTAGCGGCACTTTTTCAAAAACGCCGCTAAAACCCCAAGCATTAGCGGCACATTTTCAAAAACGC
* * * *
40459855 CGCTAAAATCCCGAGCATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAACACC-AAGCA
66 CGCTAAAACCCCAAGCACTAGCGGCGCTTTTTAAAAAACACCGCTAAAACACCGAA-CA
* *
40459913 TTAGCGACACTTTTTCAAAAACGCCGCTAAAGCCCCCAA-CATTAGCGGCACATTTTCAAAAACG
1 TTAGCGGCACTTTTTCAAAAACGCCGCTAAA-ACCCCAAGCATTAGCGGCACATTTTCAAAAACG
* *
40459977 CCGCTAAAACCCCAAGCACTAGCGGCGTTTTTTAAAAAATACCGCTAAAACACCGAACA
65 CCGCTAAAACCCCAAGCACTAGCGGCGCTTTTTAAAAAACACCGCTAAAACACCGAACA
* *
40460036 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCAAGCATTAGCGGCGCATTTTCAAAAACGC
1 TTAGCGGCACTTTTTCAAAAACGCCGCTAAAACCCCAAGCATTAGCGGCACATTTTCAAAAACGC
* *
40460101 AGCTAAAGCCCC
66 CGCTAAAACCCC
40460113 GAAAGGTAAG
Statistics
Matches: 175, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
122 6 0.03
123 162 0.93
124 7 0.04
ACGTcount: A:0.35, C:0.29, G:0.15, T:0.21
Consensus pattern (123 bp):
TTAGCGGCACTTTTTCAAAAACGCCGCTAAAACCCCAAGCATTAGCGGCACATTTTCAAAAACGC
CGCTAAAACCCCAAGCACTAGCGGCGCTTTTTAAAAAACACCGCTAAAACACCGAACA
Found at i:40460115 original size:82 final size:82
Alignment explanation
Indices: 40459790--40460115 Score: 409
Period size: 82 Copynumber: 4.0 Consensus size: 82
40459780 TAAAATGTTT
* * * * *
40459790 TTAGCGGCTCTTTTTCAAAAACACTGCTAAAACCCTAAGCATTAGCGGCACTTTTTAAAAAATAC
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCAAGCATTAGCGGCACTTTTTAAAAAACAC
* *
40459855 CGCTAAAATCCCGAGCA
66 CGCTAAAACCCCGAACA
* * * * *
40459872 TTAGCGGCGCTTTTTAAAAAACGCCGCTAAAACACCAAGCATTAGCGACACTTTTTCAAAAACGC
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCAAGCATTAGCGGCACTTTTTAAAAAACAC
* *
40459937 CGCTAAAGCCCCCAACA
66 CGCTAAAACCCCGAACA
* * * ** *
40459954 TTAGCGGCACATTTTCAAAAACGCCGCTAAAACCCCAAGCACTAGCGGCGTTTTTTAAAAAATAC
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCAAGCATTAGCGGCACTTTTTAAAAAACAC
*
40460019 CGCTAAAACACCGAACA
66 CGCTAAAACCCCGAACA
* * * *
40460036 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCAAGCATTAGCGGCGCATTTTCAAAAACGC
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCAAGCATTAGCGGCACTTTTTAAAAAACAC
* *
40460101 AGCTAAAGCCCCGAA
66 CGCTAAAACCCCGAA
40460116 AGGTAAGAAA
Statistics
Matches: 205, Mismatches: 39, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
82 205 1.00
ACGTcount: A:0.35, C:0.29, G:0.15, T:0.21
Consensus pattern (82 bp):
TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCAAGCATTAGCGGCACTTTTTAAAAAACAC
CGCTAAAACCCCGAACA
Found at i:40460209 original size:39 final size:40
Alignment explanation
Indices: 40460147--40460271 Score: 128
Period size: 40 Copynumber: 3.1 Consensus size: 40
40460137 GGGCTTTGAT
* * *
40460147 TTTTTA-CGGCGTTTTTCTGAAAAACGCCGCGAATGCTC-A
1 TTTTTAGCGGCGTTTTTC-AAAAAACACCGCTAATGCTCGA
* *
40460186 TTTTTAGCGGTGTTTTTCAAAAAATACCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTTCAAAAAACACCGCTAATGCTCGA
* * * * * *
40460226 TCTTTAGTGGCGATTTCCATAAAGCACCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTTCAAAAAACACCGCTAATGCTCGA
40460266 TTTTTA
1 TTTTTA
40460272 CCGGTATTTT
Statistics
Matches: 70, Mismatches: 14, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
39 22 0.31
40 48 0.69
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTTCAAAAAACACCGCTAATGCTCGA
Found at i:40463619 original size:36 final size:36
Alignment explanation
Indices: 40463536--40463655 Score: 125
Period size: 36 Copynumber: 3.4 Consensus size: 36
40463526 TATACTCTCT
* * * *
40463536 ATTTGGTGTGTTTCGGTTGGACTAGCTCTTATGAGC
1 ATTTGGTGTGTTTCGGATGGATTAGCTCATGTGAGC
* * * *
40463572 A-TTAGTGTGTTTTGGATGGATTGGCTCGTGTGAGC
1 ATTTGGTGTGTTTCGGATGGATTAGCTCATGTGAGC
* * *
40463607 ATTTGGTGTGTTTCGGAGGGATTAACTCATGTGATC
1 ATTTGGTGTGTTTCGGATGGATTAGCTCATGTGAGC
*
40463643 ATCTGGTGTGTTT
1 ATTTGGTGTGTTT
40463656 TGGTTGATCT
Statistics
Matches: 68, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
35 28 0.41
36 40 0.59
ACGTcount: A:0.15, C:0.11, G:0.33, T:0.42
Consensus pattern (36 bp):
ATTTGGTGTGTTTCGGATGGATTAGCTCATGTGAGC
Found at i:40464291 original size:21 final size:20
Alignment explanation
Indices: 40464246--40464319 Score: 125
Period size: 19 Copynumber: 3.8 Consensus size: 20
40464236 ATCTTCAAGG
40464246 ATATGCAATCTTAGATATG-
1 ATATGCAATCTTAGATATGT
40464265 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATG-T
40464286 ATATGCAATCTTAGATAT-T
1 ATATGCAATCTTAGATATGT
40464305 ATATGCAATCTTAGA
1 ATATGCAATCTTAGA
40464320 AGATATGATT
Statistics
Matches: 53, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
19 35 0.66
21 18 0.34
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (20 bp):
ATATGCAATCTTAGATATGT
Found at i:40464590 original size:23 final size:23
Alignment explanation
Indices: 40464546--40464590 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
40464536 TCTTTTTTTG
* *
40464546 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
40464569 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
40464591 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:40464948 original size:37 final size:37
Alignment explanation
Indices: 40464872--40464948 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 37
40464862 CATACATACG
*
40464872 TTTTATAATATATACATATACGTACACATTTTTTAATT
1 TTTTATAATATATACATATACG-ACACATTTTATAATT
* *
40464910 TTTTATAA-ATATATATATAC-ACATACTTTTATATATT
1 TTTTATAATATATACATATACGACACA-TTTTATA-ATT
40464947 TT
1 TT
40464949 CTATGTTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
35 4 0.12
36 6 0.18
37 16 0.47
38 8 0.24
ACGTcount: A:0.38, C:0.09, G:0.01, T:0.52
Consensus pattern (37 bp):
TTTTATAATATATACATATACGACACATTTTATAATT
Found at i:40464976 original size:18 final size:18
Alignment explanation
Indices: 40464944--40464988 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
40464934 ACTTTTATAT
*
40464944 ATTTTCTAT-GTTTCATA
1 ATTTTATATAGTTTCATA
40464961 ATTTTATATAGTTTCATA
1 ATTTTATATAGTTTCATA
40464979 ATTTTATATA
1 ATTTTATATA
40464989 CATACTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 8 0.31
18 18 0.69
ACGTcount: A:0.31, C:0.07, G:0.04, T:0.58
Consensus pattern (18 bp):
ATTTTATATAGTTTCATA
Found at i:40473324 original size:19 final size:18
Alignment explanation
Indices: 40473278--40473325 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
40473268 GATAGAATTT
*
40473278 TTGTCATAAAATAATTAAT
1 TTGT-ATAAAATAATTAAA
*
40473297 TTTTATAAAATAATTAAA
1 TTGTATAAAATAATTAAA
40473315 TTGTATTAAAA
1 TTGTA-TAAAA
40473326 ATTTGAACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (18 bp):
TTGTATAAAATAATTAAA
Found at i:40477410 original size:35 final size:35
Alignment explanation
Indices: 40477371--40477527 Score: 118
Period size: 36 Copynumber: 4.4 Consensus size: 35
40477361 TACTTTATGT
** *
40477371 TTGGTGTGTTTTGGTTGGACTAGCTCTTATGAGCA
1 TTGGTGTGTTTTGGAGGGACTAGCTCATATGAGCA
* * *
40477406 TTGGTGTGTTTTGGAGGGATTGGCTCATGTGAGCA
1 TTGGTGTGTTTTGGAGGGACTAGCTCATATGAGCA
** * * * *
40477441 TCTGGTGTGTTTCAGAGGGATTGGCTCGTGTGAGCA
1 T-TGGTGTGTTTTGGAGGGACTAGCTCATATGAGCA
* * * * *
40477477 TCTGGTGTGTTTCT-GAGGGATTGGCTCGTGTGATCA
1 T-TGGTGTGTTT-TGGAGGGACTAGCTCATATGAGCA
40477513 TCTGGTGTGTTTTGG
1 T-TGGTGTGTTTTGG
40477528 TTGATTTGAC
Statistics
Matches: 108, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
35 31 0.29
36 77 0.71
ACGTcount: A:0.12, C:0.11, G:0.37, T:0.39
Consensus pattern (35 bp):
TTGGTGTGTTTTGGAGGGACTAGCTCATATGAGCA
Found at i:40477459 original size:36 final size:36
Alignment explanation
Indices: 40477400--40477524 Score: 198
Period size: 36 Copynumber: 3.5 Consensus size: 36
40477390 CTAGCTCTTA
** *
40477400 TGAGCAT-TGGTGTGTTTTGGAGGGATTGGCTCATG
1 TGAGCATCTGGTGTGTTTCAGAGGGATTGGCTCGTG
40477435 TGAGCATCTGGTGTGTTTCAGAGGGATTGGCTCGTG
1 TGAGCATCTGGTGTGTTTCAGAGGGATTGGCTCGTG
*
40477471 TGAGCATCTGGTGTGTTTCTGAGGGATTGGCTCGTG
1 TGAGCATCTGGTGTGTTTCAGAGGGATTGGCTCGTG
*
40477507 TGATCATCTGGTGTGTTT
1 TGAGCATCTGGTGTGTTT
40477525 TGGTTGATTT
Statistics
Matches: 84, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 7 0.08
36 77 0.92
ACGTcount: A:0.13, C:0.12, G:0.38, T:0.38
Consensus pattern (36 bp):
TGAGCATCTGGTGTGTTTCAGAGGGATTGGCTCGTG
Found at i:40480034 original size:16 final size:17
Alignment explanation
Indices: 40479999--40480041 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
40479989 AAACATTTTA
*
40479999 AATTAAATTTAATTAATT
1 AATT-AATTTAATCAATT
40480017 AATTAATTT-ATCAATT
1 AATTAATTTAATCAATT
*
40480033 AAATAATTT
1 AATTAATTT
40480042 TCTTGATCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 14 0.61
17 5 0.22
18 4 0.17
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTAATTTAATCAATT
Found at i:40492460 original size:30 final size:31
Alignment explanation
Indices: 40492424--40492491 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 31
40492414 TTTGAGGGGA
*
40492424 TGAAAATCAAATTATATAT-CTTTATTATAG
1 TGAAAATCAAATTATATATACTTCATTATAG
* *
40492454 TGAAAATTAAATTATATATAGTTCATTATAG
1 TGAAAATCAAATTATATATACTTCATTATAG
*
40492485 TAAAAAT
1 TGAAAAT
40492492 ATAGTTTTAT
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:0.47, C:0.04, G:0.07, T:0.41
Consensus pattern (31 bp):
TGAAAATCAAATTATATATACTTCATTATAG
Found at i:40495265 original size:4 final size:4
Alignment explanation
Indices: 40495251--40495284 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
40495241 TTTTTTATCT
*
40495251 TTTA TTTTA TTTA TTTA TTCA TTTA TTTA TTTA T
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
40495285 CTATCATGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:40506097 original size:18 final size:17
Alignment explanation
Indices: 40506070--40506103 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
40506060 TTTACCTAAA
*
40506070 AAGGGAGAGGACAACTC
1 AAGGGAGAGGAAAACTC
40506087 AAGGCGAGAGGAAAACT
1 AAGG-GAGAGGAAAACT
40506104 TGCCTAATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.44, C:0.15, G:0.35, T:0.06
Consensus pattern (17 bp):
AAGGGAGAGGAAAACTC
Found at i:40507168 original size:137 final size:137
Alignment explanation
Indices: 40506948--40507391 Score: 474
Period size: 137 Copynumber: 3.3 Consensus size: 137
40506938 AATAGATCAG
* * * *
40506948 TGAAACTACAAATTCTATACCCTTGAAGTTGTAGTGGGTCGGATTGAAGTC-ACCATAACGAATC
1 TGAAACTACAAATCCTACACCCCTGAAGTTGTAGTGGGACGGATTGAA-TCTACCAT-ACGAATC
* *
40507012 TTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCTATAAATCTTATC-CCCTAAAGTTGCAGT
64 TTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCTACAAATCTTATCTCCCTAAAGTTGTAGT
*
40507076 GGAGTAGAT
129 GGAGCAGAT
* * *
40507085 TGAAGCTACAAATCCTACACCCCTGAAGTTGTAGTGGGACGGACTGAATCTACCATATCGAATTT
1 TGAAACTACAAATCCTACACCCCTGAAGTTGTAGTGGGACGGATTGAATCTACCATA-CGAATCT
* * *
40507150 TATCTCCCTAAAGTTGCAGTGGAGCAGATCTAAGCTACGAATCTTATCTCCCTAAAGTTGTAGTG
65 TATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCTACAAATCTTATCTCCCTAAAGTTGTAGTG
40507215 GAGCAGAT
130 GAGCAGAT
* * *** ** * ** *
40507223 TGAAACTATAAATCTTATGTCCCTGAAGTTACAGTGGAATAGATTGAAGCTA-C--A--AATCTT
1 TGAAACTACAAATCCTACACCCCTGAAGTTGTAGTGGGACGGATTGAATCTACCATACGAATCTT
* * * * *
40507283 ATCTCCTTGAAGTTGCAGTGAAGCATAAT-GAATCTACAAATCGTATCTCCCTAAAGTTGTAGTG
66 ATCTCCCTGAAGTTGCAGTGGAGCA-GATCGAAGCTACAAATCTTATCTCCCTAAAGTTGTAGTG
40507347 GAGCAGAT
130 GAGCAGAT
* * * * *
40507355 TGAAGCAACAAATCTTATC-TCCTTGAAGTTGTAGTGG
1 TGAAACTACAAATCCTA-CACCCCTGAAGTTGTAGTGG
40507392 AGTAAGATGA
Statistics
Matches: 260, Mismatches: 42, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
132 95 0.37
133 2 0.01
135 1 0.00
136 3 0.01
137 98 0.38
138 61 0.23
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (137 bp):
TGAAACTACAAATCCTACACCCCTGAAGTTGTAGTGGGACGGATTGAATCTACCATACGAATCTT
ATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCTACAAATCTTATCTCCCTAAAGTTGTAGTGG
AGCAGAT
Found at i:40507347 original size:132 final size:131
Alignment explanation
Indices: 40507008--40507442 Score: 460
Period size: 132 Copynumber: 3.3 Consensus size: 131
40506998 CACCATAACG
*
40507008 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCTATAAATCTTATC-CCCTAAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCTACAAATCTTATCTCCCTAAAGTTG
* * * * * * ** *
40507072 CAGTGGAGTAGATTGAAGCTACAAATCCTACACCCCTGAAGTTGTAGTGGGACGGACTGAATCTA
66 TAGTGGAGCAGATTGAAGCTACAAATCTTATATCCCTGAAGTTGTAGTGGAATAGA-TGAAGCTA
40507137 CCATA
130 -C--A
* * * *
40507142 TCGAATTTTATCTCCCTAAAGTTGCAGTGGAGCAGATCTAAGCTACGAATCTTATCTCCCTAAAG
1 ---AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCTACAAATCTTATCTCCCTAAAG
* * * **
40507207 TTGTAGTGGAGCAGATTGAAACTATAAATCTTATGTCCCTGAAGTTACAGTGGAATAGATTGAAG
63 TTGTAGTGGAGCAGATTGAAGCTACAAATCTTATATCCCTGAAGTTGTAGTGGAATAGA-TGAAG
40507272 CTACA
127 CTACA
* * * * *
40507277 AATCTTATCTCCTTGAAGTTGCAGTGAAGCATAAT-GAATCTACAAATCGTATCTCCCTAAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCA-GATCGAAGCTACAAATCTTATCTCCCTAAAGTT
* * * *
40507341 GTAGTGGAGCAGATTGAAGCAACAAATCTTATCTCCTTGAAGTTGTAGTGGAGTAAGATGAAGCT
65 GTAGTGGAGCAGATTGAAGCTACAAATCTTATATCCCTGAAGTTGTAGTGGAAT-AGATGAAGCT
40507406 ACA
129 ACA
* * * * * *
40507409 ACTCCTATATCCCTAAAGTTGTAGTGGATCAGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
40507443 TAAACCTATA
Statistics
Matches: 249, Mismatches: 46, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
131 2 0.01
132 131 0.53
133 5 0.02
135 1 0.00
137 49 0.20
138 61 0.24
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (131 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCTACAAATCTTATCTCCCTAAAGTTG
TAGTGGAGCAGATTGAAGCTACAAATCTTATATCCCTGAAGTTGTAGTGGAATAGATGAAGCTAC
A
Found at i:40507461 original size:44 final size:44
Alignment explanation
Indices: 40507008--40507443 Score: 396
Period size: 44 Copynumber: 9.8 Consensus size: 44
40506998 CACCATAACG
* * * *
40507008 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCTATA
1 AATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTGAAGCTACA
* *
40507052 AATCTTATC-CCCTAAAGTTGCAGTGGAGTAGATTGAAGCTACA
1 AATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTGAAGCTACA
* * * * * *
40507095 AATCCTA-CACCCCTGAAGTTGTAGTGG-GACGGACTGAATCTACCATA
1 AATCTTATC-TCCCTAAAGTTGTAGTGGAG-CAGATTGAAGCTA-C--A
* * *
40507142 TCGAATTTTATCTCCCTAAAGTTGCAGTGGAGCAGATCT-AAGCTACG
1 ---AATCTTATCTCCCTAAAGTTGTAGTGGAGCAGAT-TGAAGCTACA
* *
40507189 AATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTGAAACTATA
1 AATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTGAAGCTACA
* * ** **
40507233 AATCTTATGTCCCTGAAGTTACAGTGGAATAGATTGAAGCTACA
1 AATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTGAAGCTACA
* * * * * * *
40507277 AATCTTATCTCCTTGAAGTTGCAGTGAAGCATAATGAATCTACA
1 AATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTGAAGCTACA
* *
40507321 AATCGTATCTCCCTAAAGTTGTAGTGGAGCAGATTGAAGCAACA
1 AATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTGAAGCTACA
* * *
40507365 AATCTTATCTCCTTGAAGTTGTAGTGGAGTAAGA-TGAAGCTACA
1 AATCTTATCTCCCTAAAGTTGTAGTGGAG-CAGATTGAAGCTACA
* * * *
40507409 ACTCCTATATCCCTAAAGTTGTAGTGGATCAGATT
1 AATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATT
40507444 AAACCTATAA
Statistics
Matches: 314, Mismatches: 63, Indels: 30
0.77 0.15 0.07
Matches are distributed among these distances:
42 1 0.00
43 41 0.13
44 235 0.75
45 4 0.01
47 1 0.00
49 1 0.00
50 28 0.09
51 3 0.01
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTGAAGCTACA
Found at i:40507490 original size:88 final size:89
Alignment explanation
Indices: 40507274--40507498 Score: 215
Period size: 88 Copynumber: 2.6 Consensus size: 89
40507264 GATTGAAGCT
* * * * * * * * * *
40507274 ACAAATCTTATCTCCTTGAAGTTGCAGTGAAG-CATAATGAATCTACAAATCGTATCTCCCTAAA
1 ACAAATCCTATCTCCTTGAAGTTACAATGGAGTAAGAATGAAGCTACAACTCCTATATCCCTAAA
* *
40507338 GTTGTAGTGGAGCAGATTGAAGCA
66 GTTGTAGTGGAGCAGATTAAACCA
* ** *
40507362 ACAAATCTTATCTCCTTGAAGTTGTAGTGGAGTAAG-ATGAAGCTACAACTCCTATATCCCTAAA
1 ACAAATCCTATCTCCTTGAAGTTACAATGGAGTAAGAATGAAGCTACAACTCCTATATCCCTAAA
* *
40507426 GTTGTAGTGGATCAGATTAAACCT
66 GTTGTAGTGGAGCAGATTAAACCA
* * * *
40507450 ATAATTCCTATAC-CCTTGAGGTTACAATGG-GTTAGAATGAAGCTACAAC
1 ACAAATCCTAT-CTCCTTGAAGTTACAATGGAGTAAGAATGAAGCTACAAC
40507499 AACAAATTTT
Statistics
Matches: 114, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
87 4 0.04
88 108 0.95
89 2 0.02
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (89 bp):
ACAAATCCTATCTCCTTGAAGTTACAATGGAGTAAGAATGAAGCTACAACTCCTATATCCCTAAA
GTTGTAGTGGAGCAGATTAAACCA
Found at i:40509188 original size:3 final size:3
Alignment explanation
Indices: 40509180--40509223 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
40509170 TTTTTTGCCC
*
40509180 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
40509224 TCATTATTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:40509374 original size:16 final size:18
Alignment explanation
Indices: 40509338--40509377 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
40509328 CTAGTGTAAC
40509338 ATTT-TTTTATTTTATCT
1 ATTTATTTTATTTTATCT
40509355 -TTTATTTTA-TTTAT-T
1 ATTTATTTTATTTTATCT
40509370 ATTTATTT
1 ATTTATTT
40509378 ATCTATCATG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.05
16 15 0.71
17 5 0.24
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (18 bp):
ATTTATTTTATTTTATCT
Found at i:40510569 original size:31 final size:29
Alignment explanation
Indices: 40510504--40510580 Score: 77
Period size: 31 Copynumber: 2.6 Consensus size: 29
40510494 AAGCTATAGA
*
40510504 TTTAGTCCCTATATTTTAATTCGATCAAG
1 TTTAGTCCTTATATTTTAATTCGATCAAG
* *
40510533 TTTAGTCCTTATACTTTTCGAATT-GGTCAAT
1 TTTAGTCCTTATA-TTTT--AATTCGATCAAG
40510564 TTTAGTCC-TAGTATTTT
1 TTTAGTCCTTA-TATTTT
40510581 TTTAAAAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 12 0.29
30 10 0.24
31 15 0.37
32 4 0.10
ACGTcount: A:0.23, C:0.16, G:0.12, T:0.49
Consensus pattern (29 bp):
TTTAGTCCTTATATTTTAATTCGATCAAG
Found at i:40512550 original size:21 final size:20
Alignment explanation
Indices: 40512512--40512550 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
40512502 TTGAAATGGA
*
40512512 AAATTGGACTCTATAATAAT
1 AAATTGGACTCTAAAATAAT
*
40512532 AAATTGGATTTCTAAAATA
1 AAATTGGA-CTCTAAAATA
40512551 TTTCCAATAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (20 bp):
AAATTGGACTCTAAAATAAT
Found at i:40514452 original size:20 final size:22
Alignment explanation
Indices: 40514416--40514455 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
40514406 AAATTATGAA
40514416 TAAATCATGTAGGTATCGATAC
1 TAAATCATGTAGGTATCGATAC
40514438 TAAATCAT-T-GGTATCGAT
1 TAAATCATGTAGGTATCGAT
40514456 GATTCTCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 1 0.06
22 8 0.44
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (22 bp):
TAAATCATGTAGGTATCGATAC
Found at i:40520934 original size:19 final size:19
Alignment explanation
Indices: 40520906--40520969 Score: 101
Period size: 19 Copynumber: 3.3 Consensus size: 19
40520896 AATTTTCGAG
*
40520906 GATATACAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40520925 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40520944 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
40520965 GATAT
1 GATAT
40520970 ATACAATATT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
19 23 0.55
21 19 0.45
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:40520987 original size:19 final size:21
Alignment explanation
Indices: 40520907--40520982 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
40520897 ATTTTCGAGG
40520907 ATATACAATCTTAGATATG--
1 ATATACAATCTTAGATATGAT
*
40520926 ATATGCAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
*
40520947 ATATGCAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
*
40520968 ATATACAATATTAGA
1 ATATACAATCTTAGA
40520983 AGATACGATT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
19 18 0.35
21 34 0.65
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (21 bp):
ATATACAATCTTAGATATGAT
Found at i:40521202 original size:19 final size:21
Alignment explanation
Indices: 40521178--40521216 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
40521168 TGTTTTCTTT
*
40521178 TTTTTTTCTT-TTT-CGATTA
1 TTTTTTACTTATTTACGATTA
40521197 TTTTTTACTTATTTACGATT
1 TTTTTTACTTATTTACGATT
40521217 TTAAAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTTACTTATTTACGATTA
Found at i:40521443 original size:3 final size:3
Alignment explanation
Indices: 40521422--40521480 Score: 70
Period size: 3 Copynumber: 20.0 Consensus size: 3
40521412 GTTTTTAGTC
*
40521422 TAT T-T TAT TAAT T-T TAT TAT TAT TAT TAT TTT TAT TAT TA- TAT
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
40521465 TAT ATAT TAT TAT TAT
1 TAT -TAT TAT TAT TAT
40521481 ACCTACATAT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
2 6 0.12
3 37 0.76
4 6 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:40521481 original size:18 final size:18
Alignment explanation
Indices: 40521422--40521481 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
40521412 GTTTTTAGTC
*
40521422 TATTTTATTA-ATTTTAT
1 TATTATATTATATTTTAT
40521439 TATTATTATTAT-TTTTAT
1 TATTA-TATTATATTTTAT
*
40521457 TATTATATTATATATTAT
1 TATTATATTATATTTTAT
40521475 TATTATA
1 TATTATA
40521482 CCTACATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
17 10 0.26
18 28 0.74
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TATTATATTATATTTTAT
Found at i:40528042 original size:44 final size:44
Alignment explanation
Indices: 40527862--40528046 Score: 117
Period size: 44 Copynumber: 4.2 Consensus size: 44
40527852 AAGATTGTAG
* **
40527862 ATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGACGGTAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAA
** ** *
40527906 ATCTTATCTTTCTAAG-A-TAGTGGGAAGCAGATTTAAG-CCACCAA
1 ATCTTATCTCCCTAAGCAGTAGT-GG-AGCAGATCGAAGACGA-CAA
** * * * * * * * * * *
40527950 GCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTG-TAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA-CGACAA
*
40527994 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAA
40528038 ATCTTATCT
1 ATCTTATCT
40528047 TTCCAAGATA
Statistics
Matches: 97, Mismatches: 36, Indels: 16
0.65 0.24 0.11
Matches are distributed among these distances:
42 4 0.04
43 5 0.05
44 83 0.86
45 3 0.03
46 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.26
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAA
Found at i:40528049 original size:132 final size:132
Alignment explanation
Indices: 40527812--40528420 Score: 926
Period size: 132 Copynumber: 4.7 Consensus size: 132
40527802 ACCGGTGAAA
* * *
40527812 CACCAAGCTTTGTCTCCCTGAGAAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* * * *
40527877 GCAGTAGTGGAGCAAATCGAAGACGGTAAATCTTATCTTTCTAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
40527942 GC
131 GC
40527944 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
*
40528009 GCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
40528074 GC
131 GC
* * *
40528076 CACAAAGCCTTGTCTCCCTGAGCAGCAGTGGAGTA----G--G-TTGTAGATCCTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* * * *
40528134 GCAGTAATGGAGCAGATCGAAGACGGTAAATCTTATCTTTCCAAGATAATGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
40528199 GC
131 GC
* *
40528201 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTAAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
40528266 GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
40528331 GC
131 GC
* * * * *
40528333 CACAAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATGGCAAATCTTATCTCTCTGA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCT-A
** * *
40528398 AGTTGCAGTGGAGCAGATTAAAG
65 AGCAGTAGTGGAGCAGATCAAAG
40528421 CCGATAATCC
Statistics
Matches: 433, Mismatches: 36, Indels: 15
0.89 0.07 0.03
Matches are distributed among these distances:
125 114 0.26
126 1 0.00
128 1 0.00
131 1 0.00
132 296 0.68
133 20 0.05
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.24
Consensus pattern (132 bp):
CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
GC
Found at i:40528299 original size:44 final size:44
Alignment explanation
Indices: 40528123--40528303 Score: 107
Period size: 44 Copynumber: 4.1 Consensus size: 44
40528113 TTGTAGATCC
* *
40528123 TATCTCCCTAAGCAGTAATGGAGCAGATCGAAGACGGTAAATCT
1 TATCTCCCTAAGCAGTAATGGAGCAGATCAAAGACGGCAAATCT
* ** * ** **
40528167 TATCTTTCC-AAG-A-TAATGGGAAGCAGATTTAAGCCACCAAGCCT
1 TATC-TCCCTAAGCAGTAAT-GG-AGCAGATCAAAGACGGCAAATCT
* * * ** * * * ** * *
40528211 TGTCTCCCTGAGCAGCAGCGGAGAAGGTTAAAGATTGTAGATCT
1 TATCTCCCTAAGCAGTAATGGAGCAGATCAAAGACGGCAAATCT
*
40528255 TATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCT
1 TATCTCCCTAAGCAGTAATGGAGCAGATCAAAGACGGCAAATCT
40528299 TATCT
1 TATCT
40528304 TTCCAAGATA
Statistics
Matches: 94, Mismatches: 37, Indels: 12
0.66 0.26 0.08
Matches are distributed among these distances:
42 4 0.04
43 6 0.06
44 77 0.82
45 6 0.06
46 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (44 bp):
TATCTCCCTAAGCAGTAATGGAGCAGATCAAAGACGGCAAATCT
Found at i:40528312 original size:257 final size:257
Alignment explanation
Indices: 40527856--40528377 Score: 954
Period size: 257 Copynumber: 2.0 Consensus size: 257
40527846 AGGTTGAAGA
* * *
40527856 TTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGACGGTAAATCTTATCTTTCTAA
1 TTGTAGATCCTATCTCCCTAAGCAGTAATGGAGCAAATCGAAGACGGTAAATCTTATCTTTCCAA
* * *
40527921 GATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAA
66 GATAATGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTAAA
40527986 GATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCC
131 GATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCC
*
40528051 AAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGG
196 AAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGG
*
40528113 TTGTAGATCCTATCTCCCTAAGCAGTAATGGAGCAGATCGAAGACGGTAAATCTTATCTTTCCAA
1 TTGTAGATCCTATCTCCCTAAGCAGTAATGGAGCAAATCGAAGACGGTAAATCTTATCTTTCCAA
40528178 GATAATGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTAAA
66 GATAATGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTAAA
*
40528243 GATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCC
131 GATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCC
40528308 AAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGG
196 AAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGG
*
40528370 TTGAAGAT
1 TTGTAGAT
40528378 GGCAAATCTT
Statistics
Matches: 255, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
257 255 1.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.25
Consensus pattern (257 bp):
TTGTAGATCCTATCTCCCTAAGCAGTAATGGAGCAAATCGAAGACGGTAAATCTTATCTTTCCAA
GATAATGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTAAA
GATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCC
AAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGG
Found at i:40528450 original size:44 final size:42
Alignment explanation
Indices: 40528380--40528759 Score: 225
Period size: 44 Copynumber: 8.8 Consensus size: 42
40528370 TTGAAGATGG
40528380 CAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGC
1 CAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGC
* * * * *
40528422 CGATAATCCTATCTCTTTGAAGTTGCAGTTGAGCGGATTAAAAC
1 C-A-AATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGC
** * *** *
40528466 CTTGGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGATCGCATC
1 C--AAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGC
* * *
40528509 C-AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAGCAAG-
1 CAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGA-TTA--AAGC
* * * *
40528552 CAAGTCTTATC-CTCTTGAAGTTGCAGT-GAGGTAGACTGAAGATGG
1 CAAATCTTATCTCTC-TGAAGTTGCAGTGGA-GCAGA-TTAA-A-GC
* *
40528597 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGC
1 CAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGC
* * * * * * *
40528639 TGATAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATCAAAAC
1 -CA-AATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGC
** * *** *
40528683 CTTGGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-TCGCGT
1 C--AAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGC
* * *
40528725 CTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
1 CAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGA
40528760 CTAAGTAAAC
Statistics
Matches: 260, Mismatches: 58, Indels: 41
0.72 0.16 0.11
Matches are distributed among these distances:
40 42 0.16
41 14 0.05
42 6 0.02
43 25 0.10
44 143 0.55
45 26 0.10
46 4 0.02
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (42 bp):
CAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGC
Found at i:40528620 original size:45 final size:44
Alignment explanation
Indices: 40528379--40528842 Score: 202
Period size: 44 Copynumber: 10.7 Consensus size: 44
40528369 GTTGAAGATG
* * *
40528379 GCAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGC-C
1 GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGCAA
* ** * * *
40528423 G-ATAATCCTATCTCTTTGAAGTTGCAGTTGAGCGGATTAA--AA
1 GCA-AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAA
* ** * * *
40528465 CCTTGGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CGC-A
1 GC--AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAA
* * * *
40528507 TCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAGCAA
1 GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAA
* * * *
40528551 GCAAGTCTTATC-CTCTTGAAGTTGCAGT-GAGGTAGACTGAAG-ATG
1 GCAAATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGCA-A
* *
40528596 GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGC-T
1 GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTA-AGCAA
* * *
40528640 G-ATAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGA-TCAA--AA
1 GCA-AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGCAA
* ** * * *
40528682 CCTTGGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CGC--
1 GC--AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAA
* * *
40528723 GTCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAA
1 G-CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAA
* ** **
40528768 ACAAGGCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTAAATAA
1 GCAAATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACTAAGCAA
* * * *
40528812 ACAAATCCTGTCTCCCT-AAGTTGTAGTGGAG
1 GCAAATCTTATCTCCCTGAAGTTGCAGTGGAG
40528843 TGGGTTAGAG
Statistics
Matches: 322, Mismatches: 61, Indels: 75
0.70 0.13 0.16
Matches are distributed among these distances:
40 42 0.13
41 14 0.04
42 6 0.02
43 38 0.12
44 185 0.57
45 34 0.11
46 3 0.01
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (44 bp):
GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAA
Found at i:40528628 original size:217 final size:217
Alignment explanation
Indices: 40528371--40528805 Score: 726
Period size: 217 Copynumber: 2.0 Consensus size: 217
40528361 CGGAGTAGGT
*
40528371 TGAAGATGGCAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCT
1 TGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCT
** * * *
40528436 CTTTGAAGTTGCAGTTGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAG
66 CCCTAAAGTTGCAGTGGAGCGGATCAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAG
* * *
40528501 ATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAGCAAGCAAGTCTTATCCTC
131 ATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAACAAGGCTTATCCTC
* *
40528566 TTGAAGTTGCAGTGAGGTAGAC
196 CTGAAGTTGCAGTGAGGCAGAC
* *
40528588 TGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCTGATAATCCTATCT
1 TGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCT
40528653 CCCTAAAGTTGCAGTGGAGCGGATCAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAG
66 CCCTAAAGTTGCAGTGGAGCGGATCAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAG
* * *
40528718 ATCGCGTCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACAAGGCTTATCCTC
131 ATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAACAAGGCTTATCCTC
40528783 CTGAAGTTGCAGTGAGGCAGAC
196 CTGAAGTTGCAGTGAGGCAGAC
40528805 T
1 T
40528806 AAATAAACAA
Statistics
Matches: 202, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
217 202 1.00
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (217 bp):
TGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCT
CCCTAAAGTTGCAGTGGAGCGGATCAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAG
ATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAACAAGGCTTATCCTC
CTGAAGTTGCAGTGAGGCAGAC
Found at i:40529182 original size:21 final size:21
Alignment explanation
Indices: 40529153--40529209 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
40529143 ATTTTTGAGG
40529153 ATATACAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
*
40529174 ATATGCAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
40529195 ATATACAATCTTAGA
1 ATATACAATCTTAGA
40529210 AAATATGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (21 bp):
ATATACAATCTTAGATATGAT
Found at i:40529430 original size:19 final size:21
Alignment explanation
Indices: 40529406--40529444 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
40529396 TGTTTTCTTT
*
40529406 TTTTTTTCTT-TTT-CGATTA
1 TTTTTTACTTATTTACGATTA
40529425 TTTTTTACTTATTTACGATT
1 TTTTTTACTTATTTACGATT
40529445 TTAAAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTTACTTATTTACGATTA
Found at i:40529672 original size:3 final size:3
Alignment explanation
Indices: 40529664--40529703 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
40529654 ATTAATTTTG
*
40529664 TTA TTA TTA TTT TTA TTA TTA -TA TTA TATA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T
40529704 ACCTACATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:40529672 original size:15 final size:15
Alignment explanation
Indices: 40529648--40529702 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
40529638 GTTTTTAGTC
40529648 TATT-TTATTAATTT
1 TATTATTATTAATTT
* *
40529662 TGTTATTATTATTTT
1 TATTATTATTAATTT
40529677 TATTATTA-T-ATTAT
1 TATTATTATTAATT-T
40529691 ATATTATTATTA
1 -TATTATTATTA
40529703 TACCTACATA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
13 2 0.06
14 5 0.16
15 24 0.75
16 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TATTATTATTAATTT
Found at i:40529679 original size:12 final size:12
Alignment explanation
Indices: 40529650--40529701 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 12
40529640 TTTTAGTCTA
40529650 TTTTATTAATT-T
1 TTTTATT-ATTAT
*
40529662 TGTTATTATTAT
1 TTTTATTATTAT
40529674 TTTTATTATTAT
1 TTTTATTATTAT
40529686 ATTATATATTATTAT
1 -TT-T-TATTATTAT
40529701 T
1 T
40529702 ATACCTACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 3 0.09
12 18 0.53
13 2 0.06
14 2 0.06
15 9 0.26
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:40534545 original size:14 final size:14
Alignment explanation
Indices: 40534526--40534560 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
40534516 AATCCAAGTC
40534526 AAATAAAAAAATTA
1 AAATAAAAAAATTA
**
40534540 AAATAAATTAATTA
1 AAATAAAAAAATTA
40534554 AAATAAA
1 AAATAAA
40534561 TAACTAAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATAAAAAAATTA
Found at i:40534561 original size:14 final size:14
Alignment explanation
Indices: 40534535--40534574 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
40534525 CAAATAAAAA
40534535 AATTAAAATAAATT
1 AATTAAAATAAATT
40534549 AATTAAAATAAA-T
1 AATTAAAATAAATT
* *
40534562 AACTAAGATAAAT
1 AATTAAAATAAAT
40534575 AAAATAGAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (14 bp):
AATTAAAATAAATT
Found at i:40534574 original size:13 final size:13
Alignment explanation
Indices: 40534538--40534576 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
40534528 ATAAAAAAAT
*
40534538 TAAAATAAATTAAT
1 TAAAATAAA-TAAC
40534552 TAAAATAAATAAC
1 TAAAATAAATAAC
*
40534565 TAAGATAAATAA
1 TAAAATAAATAA
40534577 AATAGAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 14 0.61
14 9 0.39
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (13 bp):
TAAAATAAATAAC
Found at i:40534937 original size:40 final size:40
Alignment explanation
Indices: 40534893--40534979 Score: 156
Period size: 40 Copynumber: 2.2 Consensus size: 40
40534883 CACTTAATAA
*
40534893 TTATAAAAAATTTGGAATAAAAAAATAAAATAAAAAGAGC
1 TTATAAAAAATTTGCAATAAAAAAATAAAATAAAAAGAGC
*
40534933 TTATAAAAAATTTGCAATAAAAAAATAAAATAAAAATAGC
1 TTATAAAAAATTTGCAATAAAAAAATAAAATAAAAAGAGC
40534973 TTATAAA
1 TTATAAA
40534980 TAAAATATTG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.64, C:0.03, G:0.07, T:0.25
Consensus pattern (40 bp):
TTATAAAAAATTTGCAATAAAAAAATAAAATAAAAAGAGC
Found at i:40536860 original size:15 final size:15
Alignment explanation
Indices: 40536842--40536875 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
40536832 ATAAATGTCG
40536842 CAATAACAAATACAA
1 CAATAACAAATACAA
*
40536857 CAATAATAAATACAA
1 CAATAACAAATACAA
40536872 CAAT
1 CAAT
40536876 GGCATAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.65, C:0.18, G:0.00, T:0.18
Consensus pattern (15 bp):
CAATAACAAATACAA
Found at i:40536901 original size:13 final size:14
Alignment explanation
Indices: 40536882--40536919 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
40536872 CAATGGCATA
40536882 GAAATAATATAAAC
1 GAAATAATATAAAC
40536896 -AAATAA-ATAAAC
1 GAAATAATATAAAC
40536908 GAAACTAATATA
1 GAAA-TAATATA
40536920 CATAAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.29
13 9 0.43
14 3 0.14
15 3 0.14
ACGTcount: A:0.66, C:0.08, G:0.05, T:0.21
Consensus pattern (14 bp):
GAAATAATATAAAC
Found at i:40540937 original size:195 final size:197
Alignment explanation
Indices: 40540597--40540995 Score: 658
Period size: 195 Copynumber: 2.0 Consensus size: 197
40540587 TAATAATGTA
*
40540597 ACAATTTATCCAATCATCATTTTGTTTAATTCACATCTCGTCAATTCAATTCATTGTTCAAATCA
1 ACAATTTATCCAATCATCATTTTGTTTAATTCACATCTCATCAATTCAATTCATTG-----AT-A
40540662 TCAAATCATCACATAGCAAATTTTATTTCAACCCAATTCAAAGTCAATTCCATAATTTCATCGAA
60 TCAAATCATCACATAGCAAATTTTATTTCAACCCAATTCAAAGTCAATTCCATAATTTCATCGAA
* *
40540727 TTTCACTATTTTCAATTCTATTTAATTTACTCCTCCATCTCAAAAATTAAACATTTAGATACTAA
125 TTTCACTATTTTCAATCCTATTTAATTTACTCCTCCATCTCAAAAATTAAACATTTAGATACCAA
40540792 TTCAATTC
190 TTCAATTC
40540800 ACAATTTATCCAATCATCATTTTGTTTAATTCACATCTCATCAATTCAATTCATTG-T-TCAAAT
1 ACAATTTATCCAATCATCATTTTGTTTAATTCACATCTCATCAATTCAATTCATTGATATCAAAT
*
40540863 CATCACATAGCAAATTTTATTTCAACCCAATTCAAAGTTAATTCCATAATTTCATCGAATTTCAC
66 CATCACATAGCAAATTTTATTTCAACCCAATTCAAAGTCAATTCCATAATTTCATCGAATTTCAC
* * * *
40540928 TATTTTCAATCCTATTTAATTTAGTTCTCCATCTCAAAAATTAAACTTTTATATACCAATTCAAT
131 TATTTTCAATCCTATTTAATTTACTCCTCCATCTCAAAAATTAAACATTTAGATACCAATTCAAT
40540993 TC
196 TC
40540995 A
1 A
40540996 ACTAATCAAT
Statistics
Matches: 188, Mismatches: 8, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
195 132 0.70
197 1 0.01
203 55 0.29
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.40
Consensus pattern (197 bp):
ACAATTTATCCAATCATCATTTTGTTTAATTCACATCTCATCAATTCAATTCATTGATATCAAAT
CATCACATAGCAAATTTTATTTCAACCCAATTCAAAGTCAATTCCATAATTTCATCGAATTTCAC
TATTTTCAATCCTATTTAATTTACTCCTCCATCTCAAAAATTAAACATTTAGATACCAATTCAAT
TC
Found at i:40549689 original size:28 final size:30
Alignment explanation
Indices: 40549658--40549718 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 30
40549648 TGATATTGAT
40549658 TTAGTTA-TTGATTAATATG-TTATGTT-TG
1 TTAGTTAGTTG-TTAATATGATTATGTTATG
* *
40549686 TTAGTTAGTTGTTTATATGATTTTGTTATG
1 TTAGTTAGTTGTTAATATGATTATGTTATG
40549716 TTA
1 TTA
40549719 CATTTGAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 14 0.50
29 9 0.32
30 5 0.18
ACGTcount: A:0.23, C:0.00, G:0.18, T:0.59
Consensus pattern (30 bp):
TTAGTTAGTTGTTAATATGATTATGTTATG
Found at i:40550700 original size:45 final size:44
Alignment explanation
Indices: 40550620--40550789 Score: 132
Period size: 44 Copynumber: 3.8 Consensus size: 44
40550610 TGATTTGAGA
* * *
40550620 AAAAGGAAAGACCAT-GATTGAAAGAT-GTCAAGGCATTATAATTG
1 AAAAGGAAAGACCATAG-TTGAAAGATACT-ATGGCATTATAATCG
* *
40550664 AAAAGGAAAAGAGCATGGTTGAAAGATACTATGGCATTA-AATCGG
1 AAAAGG-AAAGACCATAGTTGAAAGATACTATGGCATTATAATC-G
* * * * **
40550709 AACAGGTAAGACCCTAGTTGAAAGATACTACGGCACCAT-ATCG
1 AAAAGGAAAGACCATAGTTGAAAGATACTATGGCATTATAATCG
**
40550752 AAAAACAATCAAGACCATAGTTGAAAGATACTATGGCA
1 -AAAAGGA--AAGACCATAGTTGAAAGATACTATGGCA
40550790 CCACTTTGGG
Statistics
Matches: 100, Mismatches: 18, Indels: 14
0.76 0.14 0.11
Matches are distributed among these distances:
43 1 0.01
44 40 0.40
45 31 0.31
46 28 0.28
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.20
Consensus pattern (44 bp):
AAAAGGAAAGACCATAGTTGAAAGATACTATGGCATTATAATCG
Found at i:40550735 original size:44 final size:45
Alignment explanation
Indices: 40550672--40550792 Score: 129
Period size: 46 Copynumber: 2.7 Consensus size: 45
40550662 TGAAAAGGAA
* * ** * *
40550672 AAGAGCATGGTTGAAAGATACTATGGCATTAAATCG-GAACAGGT-
1 AAGACCATAGTTGAAAGATACTATGGCACCAAATCGAAAACA-ATC
* * *
40550716 AAGACCCTAGTTGAAAGATACTACGGCACCATATCGAAAAACAATC
1 AAGACCATAGTTGAAAGATACTATGGCACCAAATCG-AAAACAATC
40550762 AAGACCATAGTTGAAAGATACTATGGCACCA
1 AAGACCATAGTTGAAAGATACTATGGCACCA
40550793 CTTTGGGATT
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
44 29 0.46
45 1 0.02
46 33 0.52
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.20
Consensus pattern (45 bp):
AAGACCATAGTTGAAAGATACTATGGCACCAAATCGAAAACAATC
Found at i:40550792 original size:24 final size:24
Alignment explanation
Indices: 40550723--40550792 Score: 58
Period size: 23 Copynumber: 3.0 Consensus size: 24
40550713 GGTAAGACCC
*
40550723 TAGTTGAAAGATACTACGGCACCA
1 TAGTTGAAAGATACTATGGCACCA
* * *
40550747 TA-TCGAAA-A-ACAATCAAG-ACCA
1 TAGTTGAAAGATACTAT--GGCACCA
40550769 TAGTTGAAAGATACTATGGCACCA
1 TAGTTGAAAGATACTATGGCACCA
40550793 CTTTGGGATT
Statistics
Matches: 33, Mismatches: 7, Indels: 12
0.63 0.13 0.23
Matches are distributed among these distances:
21 3 0.09
22 7 0.21
23 12 0.36
24 7 0.21
25 4 0.12
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
TAGTTGAAAGATACTATGGCACCA
Found at i:40551299 original size:10 final size:10
Alignment explanation
Indices: 40551284--40551311 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
40551274 TACTTTAGGT
40551284 ATGGAATGAA
1 ATGGAATGAA
40551294 ATGGAATGAA
1 ATGGAATGAA
40551304 ATGGAATG
1 ATGGAATG
40551312 TTTATATAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.32, T:0.21
Consensus pattern (10 bp):
ATGGAATGAA
Found at i:40553838 original size:13 final size:13
Alignment explanation
Indices: 40553804--40553838 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
40553794 TCAATTTAGT
*
40553804 ATTTTCTTCCAAA
1 ATTTACTTCCAAA
40553817 ATTTCACTTCCAAA
1 ATTT-ACTTCCAAA
40553831 ATTTACTT
1 ATTTACTT
40553839 TATTGATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTTACTTCCAAA
Found at i:40554347 original size:87 final size:87
Alignment explanation
Indices: 40554200--40554406 Score: 263
Period size: 87 Copynumber: 2.3 Consensus size: 87
40554190 GCTCTTAAAC
* ** * *
40554200 TTTTACAAAAAGAGCAATTAAGCCCTTCCTTTTTTTTTTGCACTCAGTTGAGTACTTGAACTTTC
1 TTTTCCAAAAA-AGCAATTAAG-CC--CCTGCTTTTTTTCCACTCAATTGAGTACTTGAACTTTC
* *
40554265 AAAATGCATCAAAAAGGCCCTCAAAC
62 AAAATGCATCAAAAAGACCCTCAAAA
* *
40554291 TTCTT-CAAAAAAGCAATTAATCCCCTGCTTTTTTTCCACTCAATTGGGTACTTGAACTTTCAAA
1 TT-TTCCAAAAAAGCAATTAAGCCCCTGCTTTTTTTCCACTCAATTGAGTACTTGAACTTTCAAA
*
40554355 ATGCATCAAAAAGACCCTTAAAA
65 ATGCATCAAAAAGACCCTCAAAA
*
40554378 TTTTCCAAAAAAGCAATTAAGCCCTTGCT
1 TTTTCCAAAAAAGCAATTAAGCCCCTGCT
40554407 CTTATTAAAA
Statistics
Matches: 103, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
86 2 0.02
87 80 0.78
89 2 0.02
90 9 0.09
91 8 0.08
92 2 0.02
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (87 bp):
TTTTCCAAAAAAGCAATTAAGCCCCTGCTTTTTTTCCACTCAATTGAGTACTTGAACTTTCAAAA
TGCATCAAAAAGACCCTCAAAA
Found at i:40554492 original size:9 final size:9
Alignment explanation
Indices: 40554450--40554501 Score: 50
Period size: 9 Copynumber: 5.3 Consensus size: 9
40554440 TTAAAATAAT
40554450 AAAATTTAGA
1 AAAATTTA-A
*
40554460 AAAATTTAT
1 AAAATTTAA
*
40554469 TAAATTCTAATA
1 AAAATT-T-A-A
40554481 AAAATTTAA
1 AAAATTTAA
40554490 AAAATTTAA
1 AAAATTTAA
40554499 AAA
1 AAA
40554502 TTAGAAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
9 18 0.51
10 10 0.29
11 2 0.06
12 5 0.14
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (9 bp):
AAAATTTAA
Found at i:40554773 original size:10 final size:10
Alignment explanation
Indices: 40554760--40554877 Score: 72
Period size: 10 Copynumber: 12.5 Consensus size: 10
40554750 CTTTATAAAA
40554760 TTTTATAATT
1 TTTTATAATT
40554770 TTTTAT-A-T
1 TTTTATAATT
* *
40554778 TTCTAT-ATA
1 TTTTATAATT
40554787 TTTTATAATT
1 TTTTATAATT
**
40554797 TTTTACGA-T
1 TTTTATAATT
**
40554806 TTTTATAAAA
1 TTTTATAATT
*
40554816 TTTTACAATT
1 TTTTATAATT
40554826 TTTT-T-ATT
1 TTTTATAATT
*
40554834 TTTTATGA-T
1 TTTTATAATT
40554843 TTTTAT-ATT
1 TTTTATAATT
*
40554852 GTTTTCTAATT
1 -TTTTATAATT
* *
40554863 TTTAATAAAT
1 TTTTATAATT
40554873 TTTTA
1 TTTTA
40554878 ATATTTGATA
Statistics
Matches: 82, Mismatches: 18, Indels: 16
0.71 0.16 0.14
Matches are distributed among these distances:
8 15 0.18
9 22 0.27
10 42 0.51
11 3 0.04
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (10 bp):
TTTTATAATT
Found at i:40554808 original size:37 final size:35
Alignment explanation
Indices: 40554767--40554851 Score: 82
Period size: 37 Copynumber: 2.3 Consensus size: 35
40554757 AAATTTTATA
*
40554767 ATTTTTTATATTTCTATATATTTTATAATTTTTTACG
1 ATTTTTTATATTT-TACA-ATTTTATAATTTTTTACG
* * * *
40554804 ATTTTTATAAAATTTTACAATTTTTTTATTTTTTATG
1 ATTTTT-T-ATATTTTACAATTTTATAATTTTTTACG
40554841 A-TTTTTATATT
1 ATTTTTTATATT
40554852 GTTTTCTAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
34 4 0.10
35 1 0.03
36 4 0.10
37 22 0.55
38 4 0.10
39 5 0.12
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (35 bp):
ATTTTTTATATTTTACAATTTTATAATTTTTTACG
Found at i:40554809 original size:19 final size:19
Alignment explanation
Indices: 40554787--40554849 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
40554777 TTTCTATATA
40554787 TTTTATAATTTTTTACGAT
1 TTTTATAATTTTTTACGAT
** *
40554806 TTTTATAAAATTTTACAAT
1 TTTTATAATTTTTTACGAT
* *
40554825 TTTT-TTATTTTTTATGAT
1 TTTTATAATTTTTTACGAT
40554843 TTTTATA
1 TTTTATA
40554850 TTGTTTTCTA
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
18 13 0.38
19 21 0.62
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTTATAATTTTTTACGAT
Found at i:40554811 original size:56 final size:58
Alignment explanation
Indices: 40554713--40554834 Score: 162
Period size: 56 Copynumber: 2.2 Consensus size: 58
40554703 ATTTACGAAA
* *
40554713 TTTATATTTCTTTACATTTTGTATAATTTTCTTACGGCTTTATAAAATTTTATAATTT
1 TTTATATTTCTATACATTTTGTATAATTTTCTTACGGCTTTATAAAATTTTACAATTT
* **
40554771 TTTATATTTCTATATA-TTT-TATAATTTT-TTACGATTTTTATAAAATTTTACAATTT
1 TTTATATTTCTATACATTTTGTATAATTTTCTTACG-GCTTTATAAAATTTTACAATTT
40554827 TTT-TATTT
1 TTTATATTT
40554835 TTTATGATTT
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
55 10 0.17
56 31 0.53
57 3 0.05
58 14 0.24
ACGTcount: A:0.29, C:0.07, G:0.03, T:0.61
Consensus pattern (58 bp):
TTTATATTTCTATACATTTTGTATAATTTTCTTACGGCTTTATAAAATTTTACAATTT
Found at i:40554847 original size:56 final size:55
Alignment explanation
Indices: 40554713--40554849 Score: 152
Period size: 56 Copynumber: 2.4 Consensus size: 55
40554703 ATTTACGAAA
* *
40554713 TTTATATTTCTTTACATTTTGTATAATTTTCTTACGGCTTTATAAAATTTTATAATTT
1 TTTATATTTC--TATATTTT-TATAATTTTCTTACGGCTTTATAAAATTTTACAATTT
**
40554771 TTTATATTTCTATATATTTTATAATTTT-TTACGATTTTTATAAAATTTTACAATTT
1 TTTATATTTCTATAT-TTTTATAATTTTCTTACG-GCTTTATAAAATTTTACAATTT
*
40554827 TTT-TATTTTTTATGATTTTTATA
1 TTTATA-TTTCTAT-ATTTTTATA
40554850 TTGTTTTCTA
Statistics
Matches: 70, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
55 7 0.10
56 48 0.69
57 5 0.07
58 10 0.14
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (55 bp):
TTTATATTTCTATATTTTTATAATTTTCTTACGGCTTTATAAAATTTTACAATTT
Found at i:40554856 original size:19 final size:18
Alignment explanation
Indices: 40554787--40554866 Score: 63
Period size: 19 Copynumber: 4.3 Consensus size: 18
40554777 TTTCTATATA
*
40554787 TTTTATAATTTTTTACGAT
1 TTTTAT-ATTTTTTACAAT
**
40554806 TTTTATAAAATTTTACAAT
1 TTTTAT-ATTTTTTACAAT
* **
40554825 TTTTTTATTTTTTATGAT
1 TTTTATATTTTTTACAAT
40554843 TTTTATATTGTTTT-CTAAT
1 TTTTATATT-TTTTAC-AAT
40554862 TTTTA
1 TTTTA
40554867 ATAAATTTTT
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
18 16 0.33
19 32 0.67
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.66
Consensus pattern (18 bp):
TTTTATATTTTTTACAAT
Found at i:40554864 original size:56 final size:56
Alignment explanation
Indices: 40554751--40554877 Score: 145
Period size: 56 Copynumber: 2.2 Consensus size: 56
40554741 TTCTTACGGC
* *
40554751 TTTATAAAATTTTATAATTTTTTATATTTCTATATATTTTATAATTTTTTACGATT
1 TTTATAAAATTTTACAATTTTTTATATTTCTATATATTTTATAATTTTTTACAATT
*
40554807 TTTATAAAATTTTACAATTTTTT-TATTT-TTTATGATTTT-TATATTGTTTT-CTAATT
1 TTTATAAAATTTTACAATTTTTTATATTTCTATAT-ATTTTATA-ATT-TTTTAC-AATT
*
40554863 TTTAATAAATTTTTA
1 TTT-ATAAAATTTTA
40554878 ATATTTGATA
Statistics
Matches: 62, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
54 6 0.10
55 14 0.23
56 32 0.52
57 10 0.16
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (56 bp):
TTTATAAAATTTTACAATTTTTTATATTTCTATATATTTTATAATTTTTTACAATT
Found at i:40555104 original size:91 final size:90
Alignment explanation
Indices: 40554951--40555149 Score: 274
Period size: 91 Copynumber: 2.2 Consensus size: 90
40554941 AATTTTAAAT
* * *
40554951 AAAAGCAGGGGCTTACTTCCTTTTTTTGAAAAAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAG
1 AAAAGCAGGGGCTTAATTCCTTTTTTTGAAAAAAGTTTGAGGGCCTTTTTAATGCATTTTGAAAG
* *
40555016 TTCAAGTACTCAATTGAGTGC-AAA
66 TTCAAGTACCCAAATGAGTGCAAAA
* * * *
40555040 AAAAGTAGGGGCTTAATTGCTCTTTTTTTTAACAAGGTTTGAGGGCCTTTTTAATGCATTTTGAA
1 AAAAGCAGGGGCTTAATT-C-CTTTTTTTGAAAAAAGTTTGAGGGCCTTTTTAATGCATTTTGAA
*
40555105 AGTTTAAGTACCCAAATGAGTGCAAAA
64 AGTTCAAGTACCCAAATGAGTGCAAAA
*
40555132 AAAAACAGGGGCTTAATT
1 AAAAGCAGGGGCTTAATT
40555150 TATTGGTACA
Statistics
Matches: 95, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
89 16 0.17
90 1 0.01
91 59 0.62
92 19 0.20
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (90 bp):
AAAAGCAGGGGCTTAATTCCTTTTTTTGAAAAAAGTTTGAGGGCCTTTTTAATGCATTTTGAAAG
TTCAAGTACCCAAATGAGTGCAAAA
Found at i:40556222 original size:21 final size:22
Alignment explanation
Indices: 40556173--40556223 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
40556163 ACCAAAATGT
40556173 AAACTT-ACTAATAGTTAAATA
1 AAACTTAACTAATAGTTAAATA
* *
40556194 AAATTTAATTAATAGTTAAA-A
1 AAACTTAACTAATAGTTAAATA
40556215 AAACTTAAC
1 AAACTTAAC
40556224 AGTTCAATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.33
Consensus pattern (22 bp):
AAACTTAACTAATAGTTAAATA
Found at i:40556316 original size:263 final size:265
Alignment explanation
Indices: 40555818--40556350 Score: 926
Period size: 263 Copynumber: 2.0 Consensus size: 265
40555808 AAGCTAAGGT
*
40555818 TGTTTCAATTTTAGGATTAAACCGAGCCTATGAGTCAAATCTAGATATACATGCAATGTAGGAGA
1 TGTTTCAATTTTAGGATTAAACCGAGCCTATGAGTCAAATCTAGATATACATGCAATGTAGAAGA
40555883 GCAAAGGTGAGTGACCAAAATGTAAACTTACTAATAGTTAAATAAAATTTTAACTAATAGTTAAA
66 GCAAAGGTGAGTGACCAAAATGTAAACTTACTAATAGTTAAATAAAATTTTAACTAATAGTT--A
*
40555948 AAAAAAACTTAACAATTCAATGACTTAAATAAAAGCTTTTGAATAGTTCAATAGCTTAAGTGAAA
129 AAAAAAACTTAACAATTCAATGACTTAAATAAAAGCTTTCGAATAGTTCAATAGCTTAAGTGAAA
40556013 AATTTCAATTAGGTTTATTTAAAATAAGAATATTAAATTTGTAATGACCCGATTTTTAGTGGTAC
194 AATTTCAATTAGGTTTATTTAAAATAAGAATATTAAATTTGTAATGACCCGATTTTTAGTGGTAC
40556078 TAGAAAA
259 TAGAAAA
* * * *
40556085 TGTTTCAATTTTAGGATTAAACCGAGCTTGTGAGTCAAGTCTAGATATACATGCTATGTAGAAGA
1 TGTTTCAATTTTAGGATTAAACCGAGCCTATGAGTCAAATCTAGATATACATGCAATGTAGAAGA
* *
40556150 GCAAAGGTGATTGACCAAAATGTAAACTTACTAATAGTTAAATAAAA-TTTAATTAATAGTT-AA
66 GCAAAGGTGAGTGACCAAAATGTAAACTTACTAATAGTTAAATAAAATTTTAACTAATAGTTAAA
* * *
40556213 AAAAACTTAACAGTTCAATGATTTAAATAAAAGCTTTCGAATAGTTCAATAGCTTAAGTGAAAAT
131 AAAAACTTAACAATTCAATGACTTAAATAAAAGCTTTCGAATAGTTCAATAGCTTAAGTGAAAAA
*
40556278 TTTCAATTAGGTTTATTTAAAATAAGAATATTAAATTTGTAATGACTCGATTTTTAGTGGTACTA
196 TTTCAATTAGGTTTATTTAAAATAAGAATATTAAATTTGTAATGACCCGATTTTTAGTGGTACTA
40556343 GAAAA
261 GAAAA
40556348 TGT
1 TGT
40556351 GGTTTCAAAA
Statistics
Matches: 254, Mismatches: 12, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
263 135 0.53
266 13 0.05
267 106 0.42
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.34
Consensus pattern (265 bp):
TGTTTCAATTTTAGGATTAAACCGAGCCTATGAGTCAAATCTAGATATACATGCAATGTAGAAGA
GCAAAGGTGAGTGACCAAAATGTAAACTTACTAATAGTTAAATAAAATTTTAACTAATAGTTAAA
AAAAACTTAACAATTCAATGACTTAAATAAAAGCTTTCGAATAGTTCAATAGCTTAAGTGAAAAA
TTTCAATTAGGTTTATTTAAAATAAGAATATTAAATTTGTAATGACCCGATTTTTAGTGGTACTA
GAAAA
Found at i:40559783 original size:13 final size:13
Alignment explanation
Indices: 40559743--40559802 Score: 52
Period size: 13 Copynumber: 4.7 Consensus size: 13
40559733 AAATAGAAAT
40559743 ATAATCAAAT-ATA
1 ATAAT-AAATAATA
* *
40559756 ACAAT-AATAACA
1 ATAATAAATAATA
*
40559768 ATAATAAATAGTA
1 ATAATAAATAATA
*
40559781 ATAAAAAATAATA
1 ATAATAAATAATA
*
40559794 ATAGTAAAT
1 ATAATAAAT
40559803 TAATTAATAG
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
11 3 0.08
12 6 0.17
13 27 0.75
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27
Consensus pattern (13 bp):
ATAATAAATAATA
Found at i:40562284 original size:12 final size:13
Alignment explanation
Indices: 40562265--40562297 Score: 52
Period size: 11 Copynumber: 2.7 Consensus size: 13
40562255 TATAATATAT
40562265 ATAATTTTTAAAA
1 ATAATTTTTAAAA
40562278 A-AA-TTTTAAAA
1 ATAATTTTTAAAA
40562289 ATAATTTTT
1 ATAATTTTT
40562298 TATAAAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
11 9 0.50
12 4 0.22
13 5 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATAATTTTTAAAA
Found at i:40562297 original size:24 final size:24
Alignment explanation
Indices: 40562265--40562312 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
40562255 TATAATATAT
*
40562265 ATAATTTTTAAAAAAATTTTAAAA
1 ATAATTTTTAAAAAAATTCTAAAA
* *
40562289 ATAATTTTTTATAAAATTCTAAAA
1 ATAATTTTTAAAAAAATTCTAAAA
40562313 TATATAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
ATAATTTTTAAAAAAATTCTAAAA
Found at i:40562359 original size:19 final size:19
Alignment explanation
Indices: 40562331--40562379 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
40562321 TATAAATTTT
*
40562331 TAAAAGTGAAAATAATATA
1 TAAAATTGAAAATAATATA
*
40562350 TAAAATTGAAAAATGATATA
1 TAAAATTG-AAAATAATATA
40562370 -AAAATTGAAA
1 TAAAATTGAAA
40562380 TTTTGAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 3 0.11
19 14 0.52
20 10 0.37
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (19 bp):
TAAAATTGAAAATAATATA
Found at i:40562428 original size:30 final size:32
Alignment explanation
Indices: 40562385--40562443 Score: 79
Period size: 30 Copynumber: 1.9 Consensus size: 32
40562375 TGAAATTTTG
*
40562385 AAAATATATTATTTT-GACTTTT-TAAAATTT
1 AAAATATATTATTTTAGAATTTTATAAAATTT
40562415 AAAATGATA-TATTTTAGAATTTTATAAAA
1 AAAAT-ATATTATTTTAGAATTTTATAAAA
40562444 AAATTATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 11 0.44
31 9 0.36
32 5 0.20
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (32 bp):
AAAATATATTATTTTAGAATTTTATAAAATTT
Found at i:40563226 original size:19 final size:20
Alignment explanation
Indices: 40563204--40563243 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
40563194 TAAAAAATTT
*
40563204 AATT-TTTTTTATTTTCAAA
1 AATTCTTTTTCATTTTCAAA
*
40563223 AATTCTTTTTCATTTTTAAA
1 AATTCTTTTTCATTTTCAAA
40563243 A
1 A
40563244 GGTTTTTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (20 bp):
AATTCTTTTTCATTTTCAAA
Found at i:40576409 original size:15 final size:15
Alignment explanation
Indices: 40576391--40576419 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40576381 ATATTGATAT
40576391 TATTTAATTTTATAA
1 TATTTAATTTTATAA
40576406 TATTTAATTTTATA
1 TATTTAATTTTATA
40576420 TTTTAACACT
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTTAATTTTATAA
Found at i:40576785 original size:12 final size:13
Alignment explanation
Indices: 40576767--40576806 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
40576757 TAAAAATCAT
40576767 AAAAA-TTATAAA
1 AAAAAGTTATAAA
* *
40576779 CAAAATTTATAAA
1 AAAAAGTTATAAA
40576792 AAAAAGTTATAAA
1 AAAAAGTTATAAA
40576805 AA
1 AA
40576807 TTTTAAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 4 0.17
13 20 0.83
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (13 bp):
AAAAAGTTATAAA
Found at i:40585893 original size:35 final size:35
Alignment explanation
Indices: 40585838--40585922 Score: 125
Period size: 35 Copynumber: 2.4 Consensus size: 35
40585828 GCCCATCCCT
*
40585838 CCAAAACACACCAAATGCTCACAAGAGCTAGTCCAA
1 CCAAAACACGCC-AATGCTCACAAGAGCTAGTCCAA
* * *
40585874 CCGAAACATGCCAATGCTCATAAGAGCTAGTCCAA
1 CCAAAACACGCCAATGCTCACAAGAGCTAGTCCAA
40585909 CCAAAACACGCCAA
1 CCAAAACACGCCAA
40585923 ATAGAGAGTA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 34 0.79
36 9 0.21
ACGTcount: A:0.42, C:0.33, G:0.13, T:0.12
Consensus pattern (35 bp):
CCAAAACACGCCAATGCTCACAAGAGCTAGTCCAA
Found at i:40589602 original size:17 final size:17
Alignment explanation
Indices: 40589580--40589612 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
40589570 TATATGTAGG
40589580 TATAATAATAATAATAT
1 TATAATAATAATAATAT
*
40589597 TATAATAATATTAATA
1 TATAATAATAATAATA
40589613 ATAACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TATAATAATAATAATAT
Found at i:40589603 original size:11 final size:12
Alignment explanation
Indices: 40589585--40589616 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
40589575 GTAGGTATAA
40589585 TAATAATAATAT
1 TAATAATAATAT
40589597 T-ATAATAATAT
1 TAATAATAATAT
40589608 TAATAATAA
1 TAATAATAA
40589617 CAAAATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAATAATAATAT
Found at i:40589624 original size:26 final size:26
Alignment explanation
Indices: 40589582--40589632 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
40589572 TATGTAGGTA
* *
40589582 TAATAATAATAATATT-ATAATAATAT
1 TAATAATAACAAAATTAATAA-AATAT
40589608 TAATAATAACAAAATTAATAAAATA
1 TAATAATAACAAAATTAATAAAATA
40589633 GACTAAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (26 bp):
TAATAATAACAAAATTAATAAAATAT
Found at i:40589876 original size:19 final size:21
Alignment explanation
Indices: 40589838--40589876 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
40589828 CCTTTTTTAA
*
40589838 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
40589859 AATCG-AAA-AAGAAAAAAA
1 AATCGTAAATAAGAAAAAAA
40589877 AGAAGACAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:40590078 original size:23 final size:22
Alignment explanation
Indices: 40590035--40590092 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
40590025 AAAGGGTATC
* *
40590035 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
40590056 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
40590079 TACATATCATATCT
1 TACAAATCATATCT
40590093 AAGATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:40590095 original size:19 final size:19
Alignment explanation
Indices: 40590048--40590126 Score: 77
Period size: 21 Copynumber: 3.8 Consensus size: 19
40590038 AAATTAAATC
*
40590048 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
40590068 TCTTCTAAGATTACATATCATA
1 ---TCTAAGATTACATATCATA
*
40590090 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
40590111 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
40590127 CTCGAAGATT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
19 14 0.28
21 18 0.36
22 7 0.14
23 11 0.22
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:40590108 original size:21 final size:21
Alignment explanation
Indices: 40590082--40590125 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
40590072 CTAAGATTAC
40590082 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
40590103 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
40590124 AT
1 AT
40590126 CCTCGAAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.39
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:40590593 original size:128 final size:129
Alignment explanation
Indices: 40590413--40590664 Score: 312
Period size: 128 Copynumber: 2.0 Consensus size: 129
40590403 AGATGAATTT
* * *
40590413 GATGCGATCTGCTCTACTGTAATTTCAGAGAGATAAGATCCATCATTCTAATCCACTCCGCTACA
1 GATGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCCAACATTCTAATCCACTCCACTACA
* * * * *
40590478 ACTTTAGGGAGATAGGATT-T-GTTTATTTAGTCTGCTCCACTGCAACTTTAGAGAGATAAGGCT
66 ACTTCAGAGAGATAGGATTATCG--GATTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGGCT
40590541 A
129 A
* ** * * * *
40590542 GATGCGTTCTGCTCT-CTGTAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCGCTTCACTGCA
1 GATGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCCAACATTCTAATCCACTCCACTACA
* *
40590606 ACTTCAGAGAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
66 ACTTCAGAGAGATAGGATTATCGGATTTAATCTGCTCCACTGCAACTTCAGAGAGATAA
40590665 AATTTGCCAT
Statistics
Matches: 104, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
128 88 0.85
129 15 0.14
130 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (129 bp):
GATGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCCAACATTCTAATCCACTCCACTACA
ACTTCAGAGAGATAGGATTATCGGATTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGGCTA
Found at i:40590615 original size:44 final size:44
Alignment explanation
Indices: 40590561--40590664 Score: 129
Period size: 44 Copynumber: 2.4 Consensus size: 44
40590551 TGCTCTCTGT
* *
40590561 AACTTCAGAGAGATAAGATCCA-AGGTTTTAATCCGCTTCACTGC
1 AACTTCAGAGAGATAAGAT-CATAGGCTTTAATCCGCTCCACTGC
* * * *
40590605 AACTTCAGAGAGATAGGATTATCGGCTTTAATCTGCTCCACTGC
1 AACTTCAGAGAGATAAGATCATAGGCTTTAATCCGCTCCACTGC
*
40590649 AACTTCAGGGAGATAA
1 AACTTCAGAGAGATAA
40590665 AATTTGCCAT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 1 0.02
44 50 0.98
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (44 bp):
AACTTCAGAGAGATAAGATCATAGGCTTTAATCCGCTCCACTGC
Found at i:40591025 original size:44 final size:43
Alignment explanation
Indices: 40590971--40591346 Score: 417
Period size: 44 Copynumber: 8.7 Consensus size: 43
40590961 GCTATTTTCC
* *
40590971 ACCTACTCCACTGCTGCTCAGGGAGATAAGG-TTCACGATCTTCA
1 ACCTATTCCACTGCTGC-CAGGGAGAT-AGGATTCACAATCTTCA
* *
40591015 ACCTATTCCACTGCTGACCAGGGAGATAGGA-CCTATAATCTTCA
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGATTC-ACAATCTTCA
* * * *
40591059 ATCTATTCCACTGCTGCCCAAGGAGATAGAATTCTCAATCTTCA
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGATTCACAATCTTCA
* * *
40591103 ACCTATTCCACTACTGAACAGGGAGATAGGATTCACAATCTTTA
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGATTCACAATCTTCA
*
40591147 ACCTATTCCACTGCTGTCCAGAGAGATAGGATT--C--T-TT-A
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGATTCACAATCTTCA
** * * *
40591185 ATATATTCCACTGCTACCTAGGGAGATAGAATTCTCAATCTTCA
1 ACCTATTCCACTGCTGCC-AGGGAGATAGGATTCACAATCTTCA
*
40591229 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTA
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGATTCACAATCTTCA
* *
40591273 ACCTATTCCACTACTGTCCAGGGAGATAGGATTCACAATCTTTA
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGATTCACAATCTTCA
40591317 ACCTATTCCACTGCTGACCAGGGAGATAGG
1 ACCTATTCCACTGCTG-CCAGGGAGATAGG
40591347 GCTGGAGTCA
Statistics
Matches: 282, Mismatches: 38, Indels: 24
0.82 0.11 0.07
Matches are distributed among these distances:
37 2 0.01
38 26 0.09
39 2 0.01
40 2 0.01
42 2 0.01
43 6 0.02
44 238 0.84
45 4 0.01
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.28
Consensus pattern (43 bp):
ACCTATTCCACTGCTGCCAGGGAGATAGGATTCACAATCTTCA
Found at i:40591211 original size:38 final size:38
Alignment explanation
Indices: 40591141--40591262 Score: 102
Period size: 38 Copynumber: 3.1 Consensus size: 38
40591131 GGATTCACAA
* * *
40591141 TCTTTAACCTATTCCACTGCTGTCCAGAGAGATAGGAT
1 TCTTTAACATATTCCACTGCTGACCAGAGAGATAGAAT
* *
40591179 TCTTTAATATATTCCACTGCT-ACCTAGGGAGATAGAATT
1 TCTTTAACATATTCCACTGCTGACC-AGAGAGATAGAA-T
* * *
40591218 CTCAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAT
1 -TC--T-TT-AACATATTCCACTGCTGACCAGAGAGATAGAAT
40591261 TC
1 TC
40591263 ACAATCTTTA
Statistics
Matches: 68, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
37 2 0.03
38 29 0.43
39 1 0.01
40 2 0.03
42 3 0.04
43 3 0.04
44 25 0.37
45 3 0.04
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (38 bp):
TCTTTAACATATTCCACTGCTGACCAGAGAGATAGAAT
Found at i:40591251 original size:126 final size:126
Alignment explanation
Indices: 40590971--40591306 Score: 469
Period size: 126 Copynumber: 2.6 Consensus size: 126
40590961 GCTATTTTCC
* * * *
40590971 ACCTACTCCACTGCTG-CTCAGGGAGATAAGG-TTCACGATCTTCAACCTATTCCACTGCTGACC
1 ACCTATTCCACTGCTGAC-CAGGGAGAT-AGGATTCACAATCTTTAACCTATTCCACTGCTGTCC
* *
40591034 AGGGAGATAGGACCTATAATCTTCAATCTATTCCACTGCTGCCCAAGGAGATAGAATTCTCAATC
64 AGGGAGATAGG----AT--TCTTCAATATATTCCACTGCTACCCAAGGAGATAGAATTCTCAATC
40591099 TTCA
123 TTCA
* *
40591103 ACCTATTCCACTACTGAACAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCAG
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCAG
* * * *
40591168 AGAGATAGGATTCTTTAATATATTCCACTGCTACCTAGGGAGATAGAATTCTCAATCTTCA
66 GGAGATAGGATTCTTCAATATATTCCACTGCTACCCAAGGAGATAGAATTCTCAATCTTCA
*
40591229 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTACTGTCCAG
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCAG
40591294 GGAGATAGGATTC
66 GGAGATAGGATTC
40591307 ACAATCTTTA
Statistics
Matches: 186, Mismatches: 16, Indels: 10
0.88 0.08 0.05
Matches are distributed among these distances:
126 119 0.64
128 2 0.01
131 3 0.02
132 62 0.33
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (126 bp):
ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCAG
GGAGATAGGATTCTTCAATATATTCCACTGCTACCCAAGGAGATAGAATTCTCAATCTTCA
Found at i:40591300 original size:170 final size:170
Alignment explanation
Indices: 40591018--40591346 Score: 509
Period size: 170 Copynumber: 1.9 Consensus size: 170
40591008 ATCTTCAACC
* * * *
40591018 TATTCCACTGCTGACCAGGGAGATAGGACCTATAATCTTCAATCTATTCCACTGCTGCCCAAGGA
1 TATTCCACTGCTGACCAGGGAGATAGAACCTACAATCTTCAACCTATTCCACTGCTGACCAAGGA
*
40591083 GATAGAATTCTCAATCTTCAACCTATTCCACTACTGAACAGGGAGATAGGATTCACAATCTTTAA
66 GATAGAATTCACAATCTTCAACCTATTCCACTACTGAACAGGGAGATAGGATTCACAATCTTTAA
*
40591148 CCTATTCCACTGCTGTCCAGAGAGATAGGATTCTTTAATA
131 CCTATTCCACTGCTGACCAGAGAGATAGGATTCTTTAATA
* *
40591188 TATTCCACTGCT-ACCTAGGGAGATAGAATTCT-CAATCTTCAACCTATTCCACTGCTGACCAGG
1 TATTCCACTGCTGACC-AGGGAGATAGAA-CCTACAATCTTCAACCTATTCCACTGCTGACCAAG
* * **
40591251 GAGATAGGATTCACAATCTTTAACCTATTCCACTACTGTCCAGGGAGATAGGATTCACAATCTTT
64 GAGATAGAATTCACAATCTTCAACCTATTCCACTACTGAACAGGGAGATAGGATTCACAATCTTT
*
40591316 AACCTATTCCACTGCTGACCAGGGAGATAGG
129 AACCTATTCCACTGCTGACCAGAGAGATAGG
40591347 GCTGGAGTCA
Statistics
Matches: 144, Mismatches: 13, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
169 3 0.02
170 139 0.97
171 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (170 bp):
TATTCCACTGCTGACCAGGGAGATAGAACCTACAATCTTCAACCTATTCCACTGCTGACCAAGGA
GATAGAATTCACAATCTTCAACCTATTCCACTACTGAACAGGGAGATAGGATTCACAATCTTTAA
CCTATTCCACTGCTGACCAGAGAGATAGGATTCTTTAATA
Found at i:40591405 original size:88 final size:88
Alignment explanation
Indices: 40591346--40591747 Score: 570
Period size: 88 Copynumber: 4.6 Consensus size: 88
40591336 AGGGAGATAG
* * * * *
40591346 GGCTGGAGTCATCAATCTGCTTCGCTGTCGGTGCAGGAAGGCATGATCTGCTATTTTTAACTTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
*
40591411 TTCGCTGCAACCTAGGGAGGCAA
66 TCCGCTGCAACCTAGGGAGGCAA
* * * * *
40591434 GGCTGGTGTCTTTGATCTGCTTCACTGTCAGTGCAGGAAGGCAATATCTGCTATTTTTAGCCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
40591499 TCCGCTGCAACCTAGGGAGGCAA
66 TCCGCTGCAACCTAGGGAGGCAA
* * * *
40591522 GGCTGGTGACTTCGATCTGCTTCGTTGTCGGTGCAGGAAGGTAAGATCTGCTATTTTTAGCCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
40591587 TCCGCTGCAACCTAGGGAGGCAA
66 TCCGCTGCAACCTAGGGAGGCAA
* *
40591610 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTTC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* *
40591675 TCCGCTGCAACCCAAGGAGGCAA
66 TCCGCTGCAACCTAGGGAGGCAA
* * * * * * *
40591698 GGCTGGTGACTTCGATCTGCTTTGCTGCCAGTACAAGAAGACAAGATCTG
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTG
40591748 TTATCTTCAC
Statistics
Matches: 283, Mismatches: 31, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 283 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.28
Consensus pattern (88 bp):
GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
TCCGCTGCAACCTAGGGAGGCAA
Found at i:40598322 original size:12 final size:14
Alignment explanation
Indices: 40598290--40598327 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
40598280 TATATGTAGG
40598290 TATAATAATATATAA
1 TATAATAATA-ATAA
40598305 TATAATAATAA-AA
1 TATAATAATAATAA
40598318 T-TAATAATAA
1 TATAATAATAA
40598328 CAAAATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.39
13 3 0.13
14 1 0.04
15 10 0.43
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TATAATAATAATAA
Found at i:40598332 original size:15 final size:15
Alignment explanation
Indices: 40598306--40598339 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
40598296 AATATATAAT
*
40598306 ATAATAATAAAATTA
1 ATAATAACAAAATTA
40598321 ATAATAACAAAATTA
1 ATAATAACAAAATTA
40598336 ATAA
1 ATAA
40598340 AATAGACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (15 bp):
ATAATAACAAAATTA
Found at i:40598587 original size:19 final size:21
Alignment explanation
Indices: 40598549--40598587 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
40598539 CCTTTTTTAA
*
40598549 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
40598570 AATCG-AAA-AAGAAAAAAA
1 AATCGTAAATAAGAAAAAAA
40598588 AAGAAAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:40598788 original size:23 final size:22
Alignment explanation
Indices: 40598745--40598802 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
40598735 AAAGGGTATC
* *
40598745 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
40598766 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
40598789 TACATATCATATCT
1 TACAAATCATATCT
40598803 AAGATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:40598805 original size:19 final size:19
Alignment explanation
Indices: 40598758--40598834 Score: 82
Period size: 19 Copynumber: 3.8 Consensus size: 19
40598748 AAATTAAATC
*
40598758 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
40598778 TCTTCTAAGATTACATATCATA
1 ---TCTAAGATTACATATCATA
* *
40598800 TCTAAGATTGCATATCATG
1 TCTAAGATTACATATCATA
*
40598819 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
40598835 CTCGAAGATT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 33 0.65
22 7 0.14
23 11 0.22
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:40601991 original size:9 final size:9
Alignment explanation
Indices: 40601979--40602027 Score: 73
Period size: 9 Copynumber: 5.6 Consensus size: 9
40601969 AATATAGTGG
40601979 TTATAATTA
1 TTATAATTA
40601988 TTATAATTA
1 TTATAATTA
*
40601997 TTATTATTA
1 TTATAATTA
*
40602006 TTATCATTA
1 TTATAATTA
40602015 TTAT-ATTA
1 TTATAATTA
40602023 TTATA
1 TTATA
40602028 CCTACATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
8 8 0.22
9 29 0.78
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (9 bp):
TTATAATTA
Done.