Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 73 of 135
Found at i:21896121 original size:62 final size:62
Alignment explanation
Indices: 21896052--21896176 Score: 232
Period size: 62 Copynumber: 2.0 Consensus size: 62
21896042 CTTGAATATC
*
21896052 TTCTTATTAGTTATGTCTTGGGTCCAAGTACCTGAATCTTCAATACAATTAATATATCATAA
1 TTCTTATTAGTTATGTCTTGGGTCCAAGTACCTGAATCTTCAAAACAATTAATATATCATAA
*
21896114 TTCTTATTAGTTATGTCTTGGGTCCAAGTGCCTGAATCTTCAAAACAATTAATATATCATAA
1 TTCTTATTAGTTATGTCTTGGGTCCAAGTACCTGAATCTTCAAAACAATTAATATATCATAA
21896176 T
1 T
21896177 AAAAAGGAGG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (62 bp):
TTCTTATTAGTTATGTCTTGGGTCCAAGTACCTGAATCTTCAAAACAATTAATATATCATAA
Found at i:21897160 original size:17 final size:18
Alignment explanation
Indices: 21897133--21897166 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
21897123 GCTTAAGGGA
21897133 ATATGCCAAAATCTTCAC
1 ATATGCCAAAATCTTCAC
21897151 ATAT-CCAAAATCTTCA
1 ATATGCCAAAATCTTCA
21897167 TGATTGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.41, C:0.26, G:0.03, T:0.29
Consensus pattern (18 bp):
ATATGCCAAAATCTTCAC
Found at i:21902173 original size:18 final size:18
Alignment explanation
Indices: 21902118--21902175 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
21902108 GTGTGCAAAT
*
21902118 TTTGGGTAATTGAATTAA
1 TTTGGTTAATTGAATTAA
* * *
21902136 TTCGGTTTA-TCAATTGAA
1 TTTGGTTAATTGAATT-AA
21902154 TTTGGTTAATTGAATTAA
1 TTTGGTTAATTGAATTAA
21902172 TTTG
1 TTTG
21902176 ATTAGGGGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
17 5 0.16
18 21 0.68
19 5 0.16
ACGTcount: A:0.29, C:0.03, G:0.19, T:0.48
Consensus pattern (18 bp):
TTTGGTTAATTGAATTAA
Found at i:21906352 original size:11 final size:11
Alignment explanation
Indices: 21906336--21906396 Score: 50
Period size: 11 Copynumber: 5.3 Consensus size: 11
21906326 AATACCATTT
21906336 TATTATTAAAA
1 TATTATTAAAA
*
21906347 TATTATCAAAA
1 TATTATTAAAA
* **
21906358 TATATAATTTATT
1 TAT-T-ATTAAAA
*
21906371 TATTATTAATA
1 TATTATTAAAA
21906382 TATTACTTAAAA
1 TATTA-TTAAAA
21906394 TAT
1 TAT
21906397 CACCAACATC
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
11 23 0.59
12 10 0.26
13 6 0.15
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (11 bp):
TATTATTAAAA
Found at i:21906767 original size:15 final size:17
Alignment explanation
Indices: 21906743--21906774 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
21906733 ATATATTTTA
21906743 TACAATTTTA-TTATTT
1 TACAATTTTATTTATTT
21906759 TACAA-TTTATTTATTT
1 TACAATTTTATTTATTT
21906775 ATTTTTGGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (17 bp):
TACAATTTTATTTATTT
Found at i:21910304 original size:28 final size:28
Alignment explanation
Indices: 21910264--21910593 Score: 279
Period size: 28 Copynumber: 12.1 Consensus size: 28
21910254 TAACTCTGAA
* *
21910264 GTAAACGCAAATGAATAAGCTGGCAAGC
1 GTAAACGAAAATGAATAAGCTGGCGAGC
*
21910292 GTAAACGAAAATGAATAAGCTGGCAAGC
1 GTAAACGAAAATGAATAAGCTGGCGAGC
*
21910320 GTAAGCGAAAATGAATAAGCTGGCGAGC
1 GTAAACGAAAATGAATAAGCTGGCGAGC
* *
21910348 GTAAACGCAAATGAATAAGATGGCGAGC
1 GTAAACGAAAATGAATAAGCTGGCGAGC
*
21910376 GTAAACGCAAAA-GAATAAG-TCGACGAGC
1 GTAAACG-AAAATGAATAAGCT-GGCGAGC
* *
21910404 GTAAACGTAAATGAATAAGCTAGCGAGC
1 GTAAACGAAAATGAATAAGCTGGCGAGC
* * * *
21910432 ATAAACGCAAATGAATAAGATGACGAGC
1 GTAAACGAAAATGAATAAGCTGGCGAGC
*** *
21910460 GTAAACG----TGTGCAAGCTGGCGAGT
1 GTAAACGAAAATGAATAAGCTGGCGAGC
*
21910484 GTAAAC-ACCAATGAATAAGCTGGCGAGC
1 GTAAACGA-AAATGAATAAGCTGGCGAGC
* * **
21910512 ATAAATGCAAAA-GAATAAGCTGATGAGC
1 GTAAACG-AAAATGAATAAGCTGGCGAGC
* *** *
21910540 ATAAACG----TGTGCAAGCTGGCAAGC
1 GTAAACGAAAATGAATAAGCTGGCGAGC
* *
21910564 GTAAACGCAAATGAATAAGCTGACGAGC
1 GTAAACGAAAATGAATAAGCTGGCGAGC
21910592 GT
1 GT
21910594 GAATGTGTGC
Statistics
Matches: 241, Mismatches: 45, Indels: 32
0.76 0.14 0.10
Matches are distributed among these distances:
24 33 0.14
27 4 0.02
28 197 0.82
29 6 0.02
30 1 0.00
ACGTcount: A:0.42, C:0.16, G:0.27, T:0.15
Consensus pattern (28 bp):
GTAAACGAAAATGAATAAGCTGGCGAGC
Found at i:21910522 original size:80 final size:80
Alignment explanation
Indices: 21910308--21910591 Score: 318
Period size: 80 Copynumber: 3.5 Consensus size: 80
21910298 GAAAATGAAT
* * * * *
21910308 AAGCTGGCAAGCGTAAGCGAAAATGAATAAGCTGGCGAGCGTAAACGCAAATGAATAAGATGGCG
1 AAGCTGGCGAGCGTAAACGCAAATGAATAAGCTGGCGAGCATAAACGCAAATGAATAAGATGACG
* ***
21910373 AGCGTAAACGCAAAAGAAT
66 AGCGTAAACG----TGTGC
* * *
21910392 AAG-TCGACGAGCGTAAACGTAAATGAATAAGCTAGCGAGCATAAACGCAAATGAATAAGATGAC
1 AAGCT-GGCGAGCGTAAACGCAAATGAATAAGCTGGCGAGCATAAACGCAAATGAATAAGATGAC
21910456 GAGCGTAAACGTGTGC
65 GAGCGTAAACGTGTGC
* * * * * * *
21910472 AAGCTGGCGAGTGTAAACACCAATGAATAAGCTGGCGAGCATAAATGCAAAAGAATAAGCTGATG
1 AAGCTGGCGAGCGTAAACGCAAATGAATAAGCTGGCGAGCATAAACGCAAATGAATAAGATGACG
*
21910537 AGCATAAACGTGTGC
66 AGCGTAAACGTGTGC
* *
21910552 AAGCTGGCAAGCGTAAACGCAAATGAATAAGCTGACGAGC
1 AAGCTGGCGAGCGTAAACGCAAATGAATAAGCTGGCGAGC
21910592 GTGAATGTGT
Statistics
Matches: 171, Mismatches: 27, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
80 103 0.60
81 1 0.01
83 1 0.01
84 66 0.39
ACGTcount: A:0.41, C:0.17, G:0.27, T:0.15
Consensus pattern (80 bp):
AAGCTGGCGAGCGTAAACGCAAATGAATAAGCTGGCGAGCATAAACGCAAATGAATAAGATGACG
AGCGTAAACGTGTGC
Found at i:21910557 original size:52 final size:52
Alignment explanation
Indices: 21910500--21910637 Score: 177
Period size: 52 Copynumber: 2.7 Consensus size: 52
21910490 ACCAATGAAT
* *
21910500 AAGCTGGCGAGCATAAATGCAAAAGAATAAGCTGATGAGCATAAACGTGTGC
1 AAGCTGGCGAGCATAAACGCAAAAGAATAAGCTGACGAGCATAAACGTGTGC
* * * * * *
21910552 AAGCTGGCAAGCGTAAACGCAAATGAATAAGCTGACGAGCGTGAATGTGTGC
1 AAGCTGGCGAGCATAAACGCAAAAGAATAAGCTGACGAGCATAAACGTGTGC
* * *
21910604 AAGCTGGCGAGCATAAACACACAAGGATAAGCTG
1 AAGCTGGCGAGCATAAACGCAAAAGAATAAGCTG
21910638 GCAAGCGTAA
Statistics
Matches: 72, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.38, C:0.17, G:0.28, T:0.16
Consensus pattern (52 bp):
AAGCTGGCGAGCATAAACGCAAAAGAATAAGCTGACGAGCATAAACGTGTGC
Found at i:21912729 original size:26 final size:26
Alignment explanation
Indices: 21912693--21912823 Score: 147
Period size: 26 Copynumber: 5.0 Consensus size: 26
21912683 TCATTCCAAA
* *
21912693 AATTTAACTCATGT-GAGCCTAGGCAG
1 AATTTAGCTCAT-TCGAGCCTAGACAG
* * * *
21912719 AATTTAGCTCATACGAGCCCAAATAG
1 AATTTAGCTCATTCGAGCCTAGACAG
* *
21912745 AGTTTAGCTCATTCAAGCCTAGACAG
1 AATTTAGCTCATTCGAGCCTAGACAG
* * *
21912771 AGTTTAGCTCATTCGAGCCCAGACAT
1 AATTTAGCTCATTCGAGCCTAGACAG
21912797 AATTTAGCTCATTCGAGCCTAGACAG
1 AATTTAGCTCATTCGAGCCTAGACAG
21912823 A
1 A
21912824 GTAACGCTTT
Statistics
Matches: 86, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
26 86 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (26 bp):
AATTTAGCTCATTCGAGCCTAGACAG
Found at i:21912824 original size:52 final size:50
Alignment explanation
Indices: 21912688--21912825 Score: 172
Period size: 52 Copynumber: 2.7 Consensus size: 50
21912678 TCAAGTCATT
* * *
21912688 CCAAA-AATTTAACTCATGT-GAGCCTAGGCAGAATTTAGCTCATACGAGC
1 CCAAATAATTTAGCTCAT-TCGAGCCTAGACAGAGTTTAGCTCATACGAGC
* *
21912737 CCAAATAGAGTTTAGCTCATTCAAGCCTAGACAGAGTTTAGCTCATTCGAGC
1 CCAAATA-A-TTTAGCTCATTCGAGCCTAGACAGAGTTTAGCTCATACGAGC
21912789 CCAGACATAATTTAGCTCATTCGAGCCTAGACAGAGT
1 CCA-A-ATAATTTAGCTCATTCGAGCCTAGACAGAGT
21912826 AACGCTTTTA
Statistics
Matches: 77, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
49 5 0.06
50 1 0.01
51 2 0.03
52 64 0.83
53 2 0.03
54 3 0.04
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (50 bp):
CCAAATAATTTAGCTCATTCGAGCCTAGACAGAGTTTAGCTCATACGAGC
Found at i:21920011 original size:16 final size:17
Alignment explanation
Indices: 21919992--21920025 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
21919982 TAATATAATT
21919992 AAAATAAAAG-ATAAAA
1 AAAATAAAAGCATAAAA
*
21920008 AAAATAATAGCATAAAA
1 AAAATAAAAGCATAAAA
21920025 A
1 A
21920026 TACCACATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.76, C:0.03, G:0.06, T:0.15
Consensus pattern (17 bp):
AAAATAAAAGCATAAAA
Found at i:21920127 original size:20 final size:23
Alignment explanation
Indices: 21920080--21920136 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
21920070 AACAAATATG
*
21920080 TAAATAATAAAATATATGAATAA
1 TAAATAATAAAATAAATGAATAA
*
21920103 AAAATAA-AAAATAAAT-AA-AA
1 TAAATAATAAAATAAATGAATAA
21920123 TAAATAACTAAAAT
1 TAAATAA-TAAAAT
21920137 CATGCAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 8 0.28
21 2 0.07
22 13 0.45
23 6 0.21
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (23 bp):
TAAATAATAAAATAAATGAATAA
Found at i:21920176 original size:37 final size:37
Alignment explanation
Indices: 21920115--21920222 Score: 129
Period size: 37 Copynumber: 3.1 Consensus size: 37
21920105 AATAAAAAAT
*
21920115 AAAT-AAAATAAATAACTAAAATCATGCAAATTATAC
1 AAATAAAAATAAATAATTAAAATCATGCAAATTATAC
* *
21920151 AAATAAAAATGAATAATTAAGATCATGCAAA-T-T--
1 AAATAAAAATAAATAATTAAAATCATGCAAATTATAC
* *
21920184 AAACAAAAATAAAT-ATTAAAATCATGCAAATTAAAC
1 AAATAAAAATAAATAATTAAAATCATGCAAATTATAC
21920220 AAA
1 AAA
21920223 AAATAATGTA
Statistics
Matches: 60, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
32 15 0.25
33 13 0.22
35 1 0.02
36 8 0.13
37 23 0.38
ACGTcount: A:0.62, C:0.09, G:0.05, T:0.24
Consensus pattern (37 bp):
AAATAAAAATAAATAATTAAAATCATGCAAATTATAC
Found at i:21920208 original size:32 final size:33
Alignment explanation
Indices: 21920119--21920224 Score: 133
Period size: 32 Copynumber: 3.1 Consensus size: 33
21920109 AAAAATAAAT
* *
21920119 AAAATAAATAACTAAAATCATGCAAATTATACAAATA
1 AAAATAAATAATTAAAATCATGCAAA-T-T--AAACA
* *
21920156 AAAATGAATAATTAAGATCATGCAAATTAAACA
1 AAAATAAATAATTAAAATCATGCAAATTAAACA
21920189 AAAATAAAT-ATTAAAATCATGCAAATTAAACA
1 AAAATAAATAATTAAAATCATGCAAATTAAACA
21920221 AAAA
1 AAAA
21920225 ATAATGTAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
32 26 0.41
33 12 0.19
35 1 0.02
36 1 0.02
37 23 0.37
ACGTcount: A:0.62, C:0.09, G:0.05, T:0.24
Consensus pattern (33 bp):
AAAATAAATAATTAAAATCATGCAAATTAAACA
Found at i:21921989 original size:98 final size:97
Alignment explanation
Indices: 21921885--21922153 Score: 294
Period size: 98 Copynumber: 2.7 Consensus size: 97
21921875 CTTCAATCTT
* * * *
21921885 TCCCTCTTTGGTTTTAGGATGTTAGATCCATCGTTATGACTCCAAT-TTATCCCTTTTCAATTTT
1 TCCCTCTTTAGTTTTAGG-TGTAAGATCCATCGTTGTGACTTCAATCTT-TCCCTTTTCAATTTT
21921949 AAGGTGTTAAATCCG-TCGTTACGACATCAACCTA
64 AAGGTGTTAAATCCGCT-GTTACGACATCAACCTA
* * *
21921983 TCCCTCTTTAGTTTTAAGGTGTAAGATCCATCGTTGTGGCTTCAATCTTTCCCTCTTCAGTTTT-
1 TCCCTCTTTAGTTTT-AGGTGTAAGATCCATCGTTGTGACTTCAATCTTTCCCTTTTCAATTTTA
* ** * *
21922047 AGATTGTTAGGTCTGCTGTTACGACTTCAACCTA
65 AG-GTGTTAAATCCGCTGTTACGACATCAACCTA
* * **
21922081 TCCCT-TTTCAATTTTATGGTGTAAGATCCACCGTTGCAACTTCAATCTTTCCCTTTTCAATTTT
1 TCCCTCTTT-AGTTTTA-GGTGTAAGATCCATCGTTGTGACTTCAATCTTTCCCTTTTCAATTTT
*
21922145 AGGGTGTTA
64 AAGGTGTTA
21922154 GGTCCATCAT
Statistics
Matches: 143, Mismatches: 21, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
97 6 0.04
98 130 0.91
99 7 0.05
ACGTcount: A:0.21, C:0.22, G:0.15, T:0.42
Consensus pattern (97 bp):
TCCCTCTTTAGTTTTAGGTGTAAGATCCATCGTTGTGACTTCAATCTTTCCCTTTTCAATTTTAA
GGTGTTAAATCCGCTGTTACGACATCAACCTA
Found at i:21922123 original size:49 final size:49
Alignment explanation
Indices: 21921847--21922187 Score: 219
Period size: 49 Copynumber: 7.0 Consensus size: 49
21921837 CTCTTTAATT
* * * * * * * **
21921847 TTTTAGGGTGTAAGATTCACCGTTGCGGCTTCAATCTTTCCCTCTTT-GG
1 TTTTAAGGTGTAAGATCCATCGTTACGACTTCAACCTATCCCT-TTTCAA
* * * **
21921896 TTTT-AGGATGTTAGATCCATCGTTATGACTCCAATTTATCCCTTTTCAA
1 TTTTAAGG-TGTAAGATCCATCGTTACGACTTCAACCTATCCCTTTTCAA
* * *
21921945 TTTTAAGGTGTTAA-ATCCGTCGTTACGACATCAACCTATCCCTCTTT-AG
1 TTTTAAGGTG-TAAGATCCATCGTTACGACTTCAACCTATCCCT-TTTCAA
** * * * * *
21921994 TTTTAAGGTGTAAGATCCATCGTTGTGGCTTCAATCTTTCCCTCTTCAG
1 TTTTAAGGTGTAAGATCCATCGTTACGACTTCAACCTATCCCTTTTCAA
* * *
21922043 TTTT-AGATTGTTAGGT-C-TGCTGTTACGACTTCAACCTATCCCTTTTCAA
1 TTTTAAG-GTGTAAGATCCAT-C-GTTACGACTTCAACCTATCCCTTTTCAA
* * * * * *
21922092 TTTTATGGTGTAAGATCCACCGTTGCAACTTCAATCTTTCCCTTTTCAA
1 TTTTAAGGTGTAAGATCCATCGTTACGACTTCAACCTATCCCTTTTCAA
* * * * * *
21922141 TTTTAGGGTGTTAGGTCCATCATTACGGCTTCAACATATCCCTTTTC
1 TTTTAAGGTGTAAGATCCATCGTTACGACTTCAACCTATCCCTTTTC
21922188 TACTTTAGGA
Statistics
Matches: 221, Mismatches: 58, Indels: 26
0.72 0.19 0.09
Matches are distributed among these distances:
47 1 0.00
48 14 0.06
49 195 0.88
50 11 0.05
ACGTcount: A:0.21, C:0.23, G:0.16, T:0.41
Consensus pattern (49 bp):
TTTTAAGGTGTAAGATCCATCGTTACGACTTCAACCTATCCCTTTTCAA
Found at i:21922134 original size:147 final size:148
Alignment explanation
Indices: 21921823--21922174 Score: 365
Period size: 147 Copynumber: 2.4 Consensus size: 148
21921813 GCATTTGCTG
* * * *
21921823 CTTCAATCTATTTCCTCTTTAATTTTTTAGGGTGTAAGATTCACCGTTGCGGCTTCAATCTTTCC
1 CTTCAATCT-TTCCCTCTTTAA-ATTTTAGGGTGTAAGATCCATCGTTGCGGCTTCAATCTTTCC
** * **
21921888 CTCTTTGGTTTTAGGATGTTAGATCCATCGTTATGACTCCAATTTATCCCTTTTCAATTTTAAGG
64 CTCTTCAGTTTTAGGATGTTAGATCCATCGTTACGACTCCAACCTATCCCTTTTCAATTTTAAGG
** *
21921953 TGTTAAATCCGTCGTTACGA
129 TGTTAAATCCACCGTTACAA
* * * * * *
21921973 CATCAACCTATCCCTCTTT-AGTTTTAAGGTGTAAGATCCATCGTTGTGGCTTCAATCTTTCCCT
1 CTTCAATCTTTCCCTCTTTAAATTTTAGGGTGTAAGATCCATCGTTGCGGCTTCAATCTTTCCCT
* * *
21922037 CTTCAGTTTTA-GATTGTTAGGT-C-TGCTGTTACGACTTCAACCTATCCCTTTTCAATTTTATG
66 CTTCAGTTTTAGGA-TGTTAGATCCAT-C-GTTACGACTCCAACCTATCCCTTTTCAATTTTAAG
*
21922099 GTG-TAAGATCCACCGTTGCAA
128 GTGTTAA-ATCCACCGTTACAA
* * * * *
21922120 CTTCAATCTTTCCCT-TTTCAATTTTAGGGTGTTAGGTCCATCATTACGGCTTCAA
1 CTTCAATCTTTCCCTCTTTAAATTTTAGGGTGTAAGATCCATCGTTGCGGCTTCAA
21922175 CATATCCCTT
Statistics
Matches: 166, Mismatches: 31, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
145 1 0.01
146 10 0.06
147 139 0.84
148 1 0.01
149 8 0.05
150 7 0.04
ACGTcount: A:0.21, C:0.22, G:0.15, T:0.41
Consensus pattern (148 bp):
CTTCAATCTTTCCCTCTTTAAATTTTAGGGTGTAAGATCCATCGTTGCGGCTTCAATCTTTCCCT
CTTCAGTTTTAGGATGTTAGATCCATCGTTACGACTCCAACCTATCCCTTTTCAATTTTAAGGTG
TTAAATCCACCGTTACAA
Found at i:21922154 original size:98 final size:98
Alignment explanation
Indices: 21921934--21922187 Score: 291
Period size: 98 Copynumber: 2.6 Consensus size: 98
21921924 CTCCAATTTA
* ** * *
21921934 TCCCTTTTCAATTTTAAGGTGTTAAATC-CGTCGTTACGACATCAACCTATCCCTCTTT-AGTTT
1 TCCCTTTTCAATTTTAGGGTGTTAGGTCGC-TCGTTACGACTTCAACCTATCCCT-TTTCAATTT
* ***
21921997 TAAGGTGTAAGATCCATCGTTGTGGCTTCAATCTT
64 TAAGGTGTAAGATCCACCGTTGCAACTTCAATCTT
* * **
21922032 TCCCTCTTCAGTTTTAGATTGTTAGGTCTGCT-GTTACGACTTCAACCTATCCCTTTTCAATTTT
1 TCCCTTTTCAATTTTAGGGTGTTAGGTC-GCTCGTTACGACTTCAACCTATCCCTTTTCAATTTT
*
21922096 ATGGTGTAAGATCCACCGTTGCAACTTCAATCTT
65 AAGGTGTAAGATCCACCGTTGCAACTTCAATCTT
* * *
21922130 TCCCTTTTCAATTTTAGGGTGTTAGGTC-CATCATTACGGCTTCAACATATCCCTTTTC
1 TCCCTTTTCAATTTTAGGGTGTTAGGTCGC-TCGTTACGACTTCAACCTATCCCTTTTC
21922188 TACTTTAGGA
Statistics
Matches: 130, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
96 1 0.01
97 4 0.03
98 123 0.95
99 1 0.01
100 1 0.01
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.41
Consensus pattern (98 bp):
TCCCTTTTCAATTTTAGGGTGTTAGGTCGCTCGTTACGACTTCAACCTATCCCTTTTCAATTTTA
AGGTGTAAGATCCACCGTTGCAACTTCAATCTT
Found at i:21933404 original size:19 final size:20
Alignment explanation
Indices: 21933380--21933417 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
21933370 TAATATAATT
21933380 AAAATAAAAG-ATAAAAATA
1 AAAATAAAAGCATAAAAATA
*
21933399 AAAATAATAGCATAAAAAT
1 AAAATAAAAGCATAAAAAT
21933418 GCCACATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (20 bp):
AAAATAAAAGCATAAAAATA
Found at i:21933563 original size:37 final size:35
Alignment explanation
Indices: 21933504--21933600 Score: 119
Period size: 33 Copynumber: 2.8 Consensus size: 35
21933494 AATAATTAAT
* *
21933504 AAATAAAT-ACTAAAATCATGCAAATTATACAAATAA
1 AAATAAATAATTAAAATCATGCAAATTAT--AAACAA
*
21933540 AAATAAATAATTAAGATCATGCAAA-T-TAAACAA
1 AAATAAATAATTAAAATCATGCAAATTATAAACAA
*
21933573 AAATAAATAATTAAAATCATGAAAATTA
1 AAATAAATAATTAAAATCATGCAAATTA
21933601 AGCAAAAAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
33 28 0.53
34 1 0.02
35 1 0.02
36 9 0.17
37 14 0.26
ACGTcount: A:0.62, C:0.08, G:0.04, T:0.26
Consensus pattern (35 bp):
AAATAAATAATTAAAATCATGCAAATTATAAACAA
Found at i:21933580 original size:33 final size:33
Alignment explanation
Indices: 21933538--21933608 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
21933528 TTATACAAAT
* *
21933538 AAAAATAAATAATTAAGATCATGCAAATTAAAC
1 AAAAATAAATAATTAAAATCATGAAAATTAAAC
*
21933571 AAAAATAAATAATTAAAATCATGAAAATTAAGC
1 AAAAATAAATAATTAAAATCATGAAAATTAAAC
21933604 AAAAA
1 AAAAA
21933609 ATAATGTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.65, C:0.07, G:0.06, T:0.23
Consensus pattern (33 bp):
AAAAATAAATAATTAAAATCATGAAAATTAAAC
Found at i:21935283 original size:26 final size:26
Alignment explanation
Indices: 21935250--21935427 Score: 187
Period size: 26 Copynumber: 6.9 Consensus size: 26
21935240 GTTCCAGAAA
* * *
21935250 TTTAGCTCATGCGAGCCCAAACAAAA
1 TTTAGCTCATACGAGCCCAGACAAAG
*
21935276 TTTAGCTCATACGATCCCAGACAAAG
1 TTTAGCTCATACGAGCCCAGACAAAG
* * *
21935302 TTTAGCTCTTACGAGCCCAGATAGAG
1 TTTAGCTCATACGAGCCCAGACAAAG
* * * *
21935328 TTTAACTCTTATGAGCCCAGACAGAG
1 TTTAGCTCATACGAGCCCAGACAAAG
* * *
21935354 TTTAACTCTTACGAGCCCAGACAGAG
1 TTTAGCTCATACGAGCCCAGACAAAG
* * *
21935380 TTTAGCTCATTCGAGCCCA-AAAAAA
1 TTTAGCTCATACGAGCCCAGACAAAG
*
21935405 TTTAGCTCATTCGAGCCCAGACA
1 TTTAGCTCATACGAGCCCAGACA
21935428 GAGTAATGTT
Statistics
Matches: 132, Mismatches: 19, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
25 22 0.17
26 110 0.83
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (26 bp):
TTTAGCTCATACGAGCCCAGACAAAG
Found at i:21935318 original size:52 final size:52
Alignment explanation
Indices: 21935250--21935431 Score: 206
Period size: 52 Copynumber: 3.5 Consensus size: 52
21935240 GTTCCAGAAA
* * * * * *
21935250 TTTAGCTCATGCGAGCCCAAACAAAATTTAGCTCATACGATCCCAGACAAAG
1 TTTAGCTCTTACGAGCCCAGACAGAGTTTAGCTCATACGAGCCCAGACAAAG
* * * * *
21935302 TTTAGCTCTTACGAGCCCAGATAGAGTTTAACTCTTATGAGCCCAGACAGAG
1 TTTAGCTCTTACGAGCCCAGACAGAGTTTAGCTCATACGAGCCCAGACAAAG
* * * *
21935354 TTTAACTCTTACGAGCCCAGACAGAGTTTAGCTCATTCGAGCCCA-AAAAAA
1 TTTAGCTCTTACGAGCCCAGACAGAGTTTAGCTCATACGAGCCCAGACAAAG
21935405 TTTAGCTCATT-CGAGCCCAGACAGAGT
1 TTTAGCTC-TTACGAGCCCAGACAGAGT
21935432 AATGTTCTTA
Statistics
Matches: 108, Mismatches: 21, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
51 26 0.24
52 82 0.76
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.24
Consensus pattern (52 bp):
TTTAGCTCTTACGAGCCCAGACAGAGTTTAGCTCATACGAGCCCAGACAAAG
Found at i:21937487 original size:97 final size:97
Alignment explanation
Indices: 21937316--21937509 Score: 284
Period size: 97 Copynumber: 2.0 Consensus size: 97
21937306 AACCTTGAAA
* * * *
21937316 AAGGGTATTCGATTATCCTGGTTTGAAGAAAAGTCGCGTCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGGTATTCGATTATCCTGATTTGAAGAAAAATCACGCCTAGTAAGTTAAGGCACAAATTTTCA
*
21937381 AAACTCGAAATAAAGGAATATTACCTCGATTT
66 AAACTCGAAATAAAGGAATATTACCTCAATTT
* *
21937413 AAGGGTATTCGATTAT-CTCGATTTGAAGAAAAATCATGCCTAGTAAGTTAAGGCACGAATTTTC
1 AAGGGTATTCGATTATCCT-GATTTGAAGAAAAATCACGCCTAGTAAGTTAAGGCACAAATTTTC
*
21937477 AAAA-TCCGAAATAAAGGAATATTGCCTCAATTT
65 AAAACT-CGAAATAAAGGAATATTACCTCAATTT
21937510 TAAATATTTT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
96 3 0.03
97 84 0.97
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (97 bp):
AAGGGTATTCGATTATCCTGATTTGAAGAAAAATCACGCCTAGTAAGTTAAGGCACAAATTTTCA
AAACTCGAAATAAAGGAATATTACCTCAATTT
Found at i:21937872 original size:29 final size:29
Alignment explanation
Indices: 21937840--21938029 Score: 165
Period size: 29 Copynumber: 6.6 Consensus size: 29
21937830 AAAATTCGAG
*
21937840 GTAAAAACGTGATTTTTGGAAGTTCGGGA
1 GTAAAAATGTGATTTTTGGAAGTTCGGGA
* *
21937869 GTAAAAATGTTATTTTTGGAAGTTCGGGG
1 GTAAAAATGTGATTTTTGGAAGTTCGGGA
* * * *
21937898 GTCAAAAA-GTGATTTTTGAAACTTTGGGG
1 GT-AAAAATGTGATTTTTGGAAGTTCGGGA
* * *
21937927 GCAAAAATGTAATTTTTGGAAGTTTAGGGA
1 GTAAAAATGTGATTTTTGGAAG-TTCGGGA
*
21937957 -TAAAAATGTAATTTTTGAGAAGTTCGGG-
1 GTAAAAATGTGATTTTTG-GAAGTTCGGGA
* * *
21937985 GT-CAAATGTGATTTTTGAAAGTT-TGGA
1 GTAAAAATGTGATTTTTGGAAGTTCGGGA
* **
21938012 GGAAAAATGAAATTTTTG
1 GTAAAAATGTGATTTTTG
21938030 AGAACTTCAA
Statistics
Matches: 131, Mismatches: 23, Indels: 15
0.78 0.14 0.09
Matches are distributed among these distances:
26 2 0.02
27 6 0.05
28 30 0.23
29 79 0.60
30 14 0.11
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.35
Consensus pattern (29 bp):
GTAAAAATGTGATTTTTGGAAGTTCGGGA
Found at i:21938995 original size:11 final size:11
Alignment explanation
Indices: 21938979--21939007 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
21938969 ATGAAACGTC
21938979 AAACTAAAATA
1 AAACTAAAATA
21938990 AAACTAAAATA
1 AAACTAAAATA
21939001 AAA-TAAA
1 AAACTAAA
21939008 TAAGTGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (11 bp):
AAACTAAAATA
Found at i:21941374 original size:78 final size:77
Alignment explanation
Indices: 21941273--21941516 Score: 319
Period size: 78 Copynumber: 3.1 Consensus size: 77
21941263 CCATGATCGA
* * * *
21941273 GGTAAGAGATTGGCTGATGATGATCTGCCCTAAGCTCGGGGT-AGAAGATAGAATGGCTACAATC
1 GGTAAGAGATTGGCTGATGATGATCTGCCCCAAGCTCAGGGTAAG-AGATCGAATGGCTGCAATC
21941337 TGCCCTAGGCTCGG
65 TGCCC-AGGCTCGG
* * * * * *
21941351 GGCAAGAAATTGGCTAATGATGATCTGCCCCAAGCTCAAGGTAAGAGATCGAATGGTTGCAATTT
1 GGTAAGAGATTGGCTGATGATGATCTGCCCCAAGCTCAGGGTAAGAGATCGAATGGCTGCAATCT
21941416 GGCCCAGGCTCGG
66 -GCCCAGGCTCGG
* * *
21941429 GGTAAGAGATTTGCTGATGATGATCTACCCCAGGCTCAGGGTAAGAGATCGAATGGCTGCAATCT
1 GGTAAGAGATTGGCTGATGATGATCTGCCCCAAGCTCAGGGTAAGAGATCGAATGGCTGCAATCT
*
21941494 ACCCCAGGCTCGG
66 -GCCCAGGCTCGG
21941507 GGTAAGAGAT
1 GGTAAGAGAT
21941517 CGAATGGCTA
Statistics
Matches: 143, Mismatches: 21, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
78 137 0.96
79 6 0.04
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (77 bp):
GGTAAGAGATTGGCTGATGATGATCTGCCCCAAGCTCAGGGTAAGAGATCGAATGGCTGCAATCT
GCCCAGGCTCGG
Found at i:21941461 original size:39 final size:39
Alignment explanation
Indices: 21941259--21941828 Score: 237
Period size: 39 Copynumber: 14.6 Consensus size: 39
21941249 GATTACAATT
* * * *
21941259 TGCCCCATGATCGAGGTAAGAGATTGGCTGATGATGATC
1 TGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGATGATC
* * * * *
21941298 TGCCCTAAGCTCGGGGTAGAAGATAGAATGGCT-A-CA--ATC
1 TGCCCCAGGCTCGGGGT--AAG--AGATTTGCTGATGATGATC
* * * * *
21941337 TGCCCTAGGCTCGGGGCAAGAAATTGGCTAATGATGATC
1 TGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGATGATC
* ** * *
21941376 TGCCCCAAGCTCAAGGTAAGAGA--T-C-GAATGGTTGCAATT
1 TGCCCCAGGCTCGGGGTAAGAGATTTGCTG-AT-GATG--ATC
*
21941415 TGGCCCAGGCTCGGGGTAAGAGATTTGCTGATGATGATC
1 TGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGATGATC
* * *
21941454 TACCCCAGGCTCAGGGTAAGAGA--T-C-GAATGGCTGCAATC
1 TGCCCCAGGCTCGGGGTAAGAGATTTGCTG-AT-GATG--ATC
* * * * **
21941493 TACCCCAGGCTCGGGGTAAGAGA-TCGAATGGCT-ACAATC
1 TGCCCCAGGCTCGGGGTAAGAGATTTG-CT-GATGATGATC
* * * * *
21941532 TGCCCCAGGCTCGGGGTAAGAGGTTGGCTAATAATGATA
1 TGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGATGATC
* **** * *
21941571 TGCCCC-GAGCTCGGGGTAAAAGATCAAATGGTTG-TAATC
1 TGCCCCAG-GCTCGGGGTAAGAGATTTGCT-GATGATGATC
*
21941610 TACCCCAGGCTCGGGGTAAGAGATTTGCTGATGATGATC
1 TGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGATGATC
* * * * * * *
21941649 TGCCCCAAGCTCGAGGTAAGAGATCTGATGGTTG-TAATA
1 TGCCCCAGGCTCGGGGTAAGAGATTTGCT-GATGATGATC
** * *
21941688 TGCTTCAGGCTTGGGGTAAGAGATTTGCTAATGATGATC
1 TGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGATGATC
* *
21941727 TGCCCCAAGCTCGAGGTAAGAGA--T-C-GAATGGATGCAATC
1 TGCCCCAGGCTCGGGGTAAGAGATTTGCTG-AT-GATG--ATC
* * * * *
21941766 TGTCCTAGGCTCGAGGTAAGAGATTGGCTGATGGTGATC
1 TGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGATGATC
* * *
21941805 TGGCCCAAGCTCGAGGTAAGAGAT
1 TGCCCCAGGCTCGGGGTAAGAGAT
21941829 CGGATCTTCG
Statistics
Matches: 391, Mismatches: 99, Indels: 82
0.68 0.17 0.14
Matches are distributed among these distances:
35 8 0.02
36 10 0.03
37 16 0.04
38 7 0.02
39 313 0.80
40 7 0.02
41 11 0.03
42 7 0.02
43 11 0.03
44 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.23
Consensus pattern (39 bp):
TGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGATGATC
Found at i:21941583 original size:78 final size:78
Alignment explanation
Indices: 21941490--21941830 Score: 405
Period size: 78 Copynumber: 4.4 Consensus size: 78
21941480 AATGGCTGCA
* * * * * *
21941490 ATCTACCCCAGGCTCGGGGTAAGAGATCGAATGGCTACAATCTGCCCCAGGCTCGGGGTAAGAGG
1 ATCTGCCCCAAGCTCGAGGTAAGAGATCGAATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGA
*
21941555 TTGGCTAATAATG
66 TTGGCTAATGATG
* * * * * * *
21941568 ATATGCCCCGAGCTCGGGGTAAAAGATCAAATGGTTGTAATCTACCCCAGGCTCGGGGTAAGAGA
1 ATCTGCCCCAAGCTCGAGGTAAGAGATCGAATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGA
* *
21941633 TTTGCTGATGATG
66 TTGGCTAATGATG
* * ** *
21941646 ATCTGCCCCAAGCTCGAGGTAAGAGATCTG-ATGGTTGTAATATGCTTCAGGCTTGGGGTAAGAG
1 ATCTGCCCCAAGCTCGAGGTAAGAGATC-GAATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAG
*
21941710 ATTTGCTAATGATG
65 ATTGGCTAATGATG
* * * *
21941724 ATCTGCCCCAAGCTCGAGGTAAGAGATCGAATGGATGCAATCTGTCCTAGGCTCGAGGTAAGAGA
1 ATCTGCCCCAAGCTCGAGGTAAGAGATCGAATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGA
* *
21941789 TTGGCTGATGGTG
66 TTGGCTAATGATG
*
21941802 ATCTGGCCCAAGCTCGAGGTAAGAGATCG
1 ATCTGCCCCAAGCTCGAGGTAAGAGATCG
21941831 GATCTTCGAT
Statistics
Matches: 223, Mismatches: 38, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
77 1 0.00
78 222 1.00
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (78 bp):
ATCTGCCCCAAGCTCGAGGTAAGAGATCGAATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGA
TTGGCTAATGATG
Found at i:21941823 original size:117 final size:117
Alignment explanation
Indices: 21941345--21941828 Score: 382
Period size: 117 Copynumber: 4.1 Consensus size: 117
21941335 TCTGCCCTAG
* * * * *
21941345 GCTCGGGGCAAGAAATTGGCTAAT-GATG-ATCTGCCCCAAGCTCAAGGTAAGAGATCGAATGGT
1 GCTCGGGGTAAGAGATT--CTAATGGATGAATCTACCCCAAGCTCGAGGTAAGAGATCGAATGGA
* * * * * * *
21941408 TGCAATTTGGCCCAGGCTCGGGGTAAGAGATTTGCTGATGATGATCTACCCCAG
64 TGCAATCTGCCCCAGGCTCGAGGTAAGAGATTGGCTGATGATGATATGCCCCAA
* * * * * *
21941462 GCTCAGGGTAAGAGA-TCGAATGGCTGCAATCTACCCCAGGCTCGGGGTAAGAGATCGAATGGCT
1 GCTCGGGGTAAGAGATTCTAATGGATG-AATCTACCCCAAGCTCGAGGTAAGAGATCGAATGGAT
* * * * * *
21941526 ACAATCTGCCCCAGGCTCGGGGTAAGAGGTTGGCTAATAATGATATGCCCCGA
65 GCAATCTGCCCCAGGCTCGAGGTAAGAGATTGGCTGATGATGATATGCCCCAA
* * * * *
21941579 GCTCGGGGTAAAAGA-TCAAATGGTTGTAATCTACCCCAGGCTCGGGGTAAGAGATTTGCTG-AT
1 GCTCGGGGTAAGAGATTCTAATGGATG-AATCTACCCCAAGCTCGAGGTAAGAGA--T-C-GAAT
* * ** *
21941642 -GATG--ATCTGCCCCAAGCTCGAGGTAAGAGA-T--CTGATGGTTGTAATATGCTTCAG
61 GGATGCAATCTGCCCCAGGCTCGAGGTAAGAGATTGGCTGAT-GATG--ATATGCCCCAA
* *
21941696 GCTTGGGGTAAGAGATTTGCTAAT-GATG-ATCTGCCCCAAGCTCGAGGTAAGAGATCGAATGGA
1 GCTCGGGGTAAGAGA-TT-CTAATGGATGAATCTACCCCAAGCTCGAGGTAAGAGATCGAATGGA
* * * * *
21941759 TGCAATCTGTCCTAGGCTCGAGGTAAGAGATTGGCTGATGGTGATCTGGCCCAA
64 TGCAATCTGCCCCAGGCTCGAGGTAAGAGATTGGCTGATGATGATATGCCCCAA
*
21941813 GCTCGAGGTAAGAGAT
1 GCTCGGGGTAAGAGAT
21941829 CGGATCTTCG
Statistics
Matches: 291, Mismatches: 56, Indels: 41
0.75 0.14 0.11
Matches are distributed among these distances:
113 1 0.00
114 11 0.04
115 10 0.03
116 3 0.01
117 242 0.83
118 1 0.00
119 10 0.03
120 12 0.04
121 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (117 bp):
GCTCGGGGTAAGAGATTCTAATGGATGAATCTACCCCAAGCTCGAGGTAAGAGATCGAATGGATG
CAATCTGCCCCAGGCTCGAGGTAAGAGATTGGCTGATGATGATATGCCCCAA
Found at i:21942853 original size:45 final size:46
Alignment explanation
Indices: 21942739--21942853 Score: 178
Period size: 46 Copynumber: 2.5 Consensus size: 46
21942729 AATTTTAGTC
*
21942739 GCCCTTTGCGGGTTTTCAACTCAAAATTCCTTTTGTTTTCAAGAAA
1 GCCCTTTGCGGGTTTTCAACTCAAAATTCATTTTGTTTTCAAGAAA
* *
21942785 GCCCTTTGCGGGTTTTCAACTCAAAATTCATTTTGTTTTC-AGGAT
1 GCCCTTTGCGGGTTTTCAACTCAAAATTCATTTTGTTTTCAAGAAA
* *
21942830 GCCCTTTACGGGTTTTCATCTCAA
1 GCCCTTTGCGGGTTTTCAACTCAA
21942854 TTTTAGGCAA
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
45 25 0.39
46 39 0.61
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.40
Consensus pattern (46 bp):
GCCCTTTGCGGGTTTTCAACTCAAAATTCATTTTGTTTTCAAGAAA
Found at i:21944007 original size:39 final size:39
Alignment explanation
Indices: 21943948--21944675 Score: 328
Period size: 39 Copynumber: 18.7 Consensus size: 39
21943938 AATGATTGCA
* * * *
21943948 ATCTGCCCCATGATCAGGGTAAGAGATTGGCTGATGATG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGATG
* * * * * *
21943987 ATTTGCCCCAAGCTCGGGGTAAAAGATCGAATG--GCTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGATG
* * * *
21944024 CAATCTACCCCAGGCTCGGGGTAAGAAATTGGCTAATGATG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGATG
* * *
21944065 ATCTGCCCCAGGCTCGGGGTAAGAGATCGAATG--GCTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGATG
* *
21944102 CAATTTGCCCCAGGCTCGGGATAAGAGATTTG-CTGATGATG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGA-TTGACTGATGATG
* ** * * * ** * * *
21944143 AGT-AGCCTTAGGCTCGAGATAAGAAATCAAATGGTTG-TA
1 A-TCTGCCCCAGGCTCGGGGTAAGAGATTGACT-GATGATG
* * * *
21944182 ATCTGCCCTAAGCTCGGGGTAA-AGGATTTACTGATAATG
1 ATCTGCCCCAGGCTCGGGGTAAGA-GATTGACTGATGATG
* * * * * *
21944221 ATCTGTCTCAAGCTCGGGGTAAGAGATCGAATG--GCTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGATG
* * * * *
21944258 CAATCTGCCCTAAGCTCGGCGTAAGAGATTTG-CTGATAACG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGA-TTGACTGATGATG
* * * *
21944299 ATCTGCCCCAGGCTTGGGGTAAGAGATCGAATG--GCTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGATG
* *
21944336 CAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTAATGATG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGATG
* * * *
21944377 ATCTGCCCCAAGCTCGGGGTAAGAGATCGAATG--GTTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGATG
* * * *
21944414 CAATCTACCCTAAGCTCGGGGTAAGAGATTTACTGATGATG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGATG
* * * * ** * *
21944455 ATCTGCCTCAGTCTCAGAGTAAGAGATCAAATG--GTTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGATG
* * *
21944492 CAATCTACCCCAAGCTCGGGGTAAGAGATTTG-TTGATGATG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGA-TTGACTGATGATG
* * * * *
21944533 ATCTG-TCTAGGCTCGGGGTAAGAGATCGAATG--GTTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGATG
* * * * * * **
21944569 CAATCTGCCTCAGGATCGGGGTAAGAGATCGAATGGTTACA
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGATG
* *
21944610 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGATG
** **
21944649 ATCTATCTTAGGCTCGGGGTAAGAGAT
1 ATCTGCCCCAGGCTCGGGGTAAGAGAT
21944676 CGGATCTTCG
Statistics
Matches: 501, Mismatches: 147, Indels: 82
0.69 0.20 0.11
Matches are distributed among these distances:
36 3 0.01
37 17 0.03
38 31 0.06
39 424 0.85
40 10 0.02
41 16 0.03
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (39 bp):
ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGATG
Found at i:21944073 original size:78 final size:78
Alignment explanation
Indices: 21943944--21944597 Score: 740
Period size: 78 Copynumber: 8.4 Consensus size: 78
21943934 TTCAAATGAT
* * * * *
21943944 TGCAATCTGCCCCATGATCAGGGTAAGAGATTGGCTGATGATGATTTGCCCCAAGCTCGGGGTAA
1 TGCAATCTGCCCCAAGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAAGCTCGGGGTAA
*
21944009 AAGATCGAATGGC
66 GAGATCGAATGGC
* * * * * *
21944022 TGCAATCTACCCCAGGCTCGGGGTAAGAAATTGGCTAATGATGATCTGCCCCAGGCTCGGGGTAA
1 TGCAATCTGCCCCAAGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAAGCTCGGGGTAA
21944087 GAGATCGAATGGC
66 GAGATCGAATGGC
* * * * ** * * *
21944100 TGCAATTTGCCCCAGGCTCGGGATAAGAGATTTGCTGATGATGAGT-AGCCTTAGGCTCGAGATA
1 TGCAATCTGCCCCAAGCTCGGGGTAAGAGATTTGCTGATGATGA-TCTGCCCCAAGCTCGGGGTA
* * *
21944164 AGAAATCAAATGGT
65 AGAGATCGAATGGC
* * * * * *
21944178 TGTAATCTGCCCTAAGCTCGGGGTAA-AGGATTTACTGATAATGATCTGTCTCAAGCTCGGGGTA
1 TGCAATCTGCCCCAAGCTCGGGGTAAGA-GATTTGCTGATGATGATCTGCCCCAAGCTCGGGGTA
21944242 AGAGATCGAATGGC
65 AGAGATCGAATGGC
* * * * * *
21944256 TGCAATCTGCCCTAAGCTCGGCGTAAGAGATTTGCTGATAACGATCTGCCCCAGGCTTGGGGTAA
1 TGCAATCTGCCCCAAGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAAGCTCGGGGTAA
21944321 GAGATCGAATGGC
66 GAGATCGAATGGC
* * *
21944334 TGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTAATGATGATCTGCCCCAAGCTCGGGGTAA
1 TGCAATCTGCCCCAAGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAAGCTCGGGGTAA
*
21944399 GAGATCGAATGGT
66 GAGATCGAATGGC
* * * * * *
21944412 TGCAATCTACCCTAAGCTCGGGGTAAGAGATTTACTGATGATGATCTGCCTC-AGTCTCAGAGTA
1 TGCAATCTGCCCCAAGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAAG-CTCGGGGTA
* *
21944476 AGAGATCAAATGGT
65 AGAGATCGAATGGC
* * * * *
21944490 TGCAATCTACCCCAAGCTCGGGGTAAGAGATTTGTTGATGATGATCTG-TCTAGGCTCGGGGTAA
1 TGCAATCTGCCCCAAGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAAGCTCGGGGTAA
*
21944554 GAGATCGAATGGT
66 GAGATCGAATGGC
* * *
21944567 TGCAATCTGCCTCAGGATCGGGGTAAGAGAT
1 TGCAATCTGCCCCAAGCTCGGGGTAAGAGAT
21944598 CGAATGGTTA
Statistics
Matches: 489, Mismatches: 81, Indels: 13
0.84 0.14 0.02
Matches are distributed among these distances:
77 51 0.10
78 436 0.89
79 2 0.00
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.24
Consensus pattern (78 bp):
TGCAATCTGCCCCAAGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAAGCTCGGGGTAA
GAGATCGAATGGC
Found at i:21949027 original size:97 final size:97
Alignment explanation
Indices: 21948856--21949049 Score: 307
Period size: 97 Copynumber: 2.0 Consensus size: 97
21948846 AACCTTGAAA
* *
21948856 AAGGGTATTCGATTATCCCGGTTTGAAGAAAAGTCACGCCTAGTAAGTTGAGGCACAAATTTTCA
1 AAGGGTATTCGATTATCCCGGTTTGAAGAAAAATCACGCCTAGTAAGTTAAGGCACAAATTTTCA
* *
21948921 AAACTCGAAATAAAGGAATATTACCTCGATTT
66 AAACCCGAAATAAAAGAATATTACCTCGATTT
** *
21948953 AAGGGTATTCGATTATCCCGGTTTGAAGAAAAATCGTGCCTAGTAAGTTAAGGCACGAATTTTCA
1 AAGGGTATTCGATTATCCCGGTTTGAAGAAAAATCACGCCTAGTAAGTTAAGGCACAAATTTTCA
* *
21949018 AGACCCGAAATAAAAGAATATTGCCTCGATTT
66 AAACCCGAAATAAAAGAATATTACCTCGATTT
21949050 TAAATATTTT
Statistics
Matches: 88, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
97 88 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (97 bp):
AAGGGTATTCGATTATCCCGGTTTGAAGAAAAATCACGCCTAGTAAGTTAAGGCACAAATTTTCA
AAACCCGAAATAAAAGAATATTACCTCGATTT
Found at i:21949194 original size:14 final size:15
Alignment explanation
Indices: 21949175--21949221 Score: 64
Period size: 14 Copynumber: 3.3 Consensus size: 15
21949165 AAGAATGAAC
21949175 AAATATACG-AAAAT
1 AAATATACGAAAAAT
21949189 AAATATGA-GAAAAAT
1 AAATAT-ACGAAAAAT
21949204 AAA-ATACGAAAAAT
1 AAATATACGAAAAAT
21949218 AAAT
1 AAAT
21949222 GAGAAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.03
14 19 0.66
15 9 0.31
ACGTcount: A:0.68, C:0.04, G:0.09, T:0.19
Consensus pattern (15 bp):
AAATATACGAAAAAT
Found at i:21949234 original size:27 final size:28
Alignment explanation
Indices: 21949179--21949233 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
21949169 ATGAACAAAT
21949179 ATACGAAAATAAATATGAGAAAAATAAA
1 ATACGAAAATAAATATGAGAAAAATAAA
21949207 ATACGAAAA-ATAA-ATGAG-AAAATAAA
1 ATACGAAAATA-AATATGAGAAAAATAAA
21949233 A
1 A
21949234 AATTAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 9 0.35
27 6 0.23
28 11 0.42
ACGTcount: A:0.69, C:0.04, G:0.11, T:0.16
Consensus pattern (28 bp):
ATACGAAAATAAATATGAGAAAAATAAA
Found at i:21949412 original size:28 final size:28
Alignment explanation
Indices: 21949355--21949541 Score: 170
Period size: 29 Copynumber: 6.6 Consensus size: 28
21949345 AAAGTTTTAG
* * *
21949355 GGGTAAAAATGTCATTTTAGGAAAATTCA
1 GGGTAAAAATGTAATTTTTGG-AAGTTCA
*
21949384 GGGTAAAAATGTGATTTTTGGAAGTTCA
1 GGGTAAAAATGTAATTTTTGGAAGTTCA
*
21949412 GGGGTAAAAATGTGATTTTTGGAAGTTC-
1 -GGGTAAAAATGTAATTTTTGGAAGTTCA
21949440 GGG-AGCAAAATGT-ATTTTTGGAAGTTCGA
1 GGGTA--AAAATGTAATTTTTGGAAGTTC-A
* * *
21949469 GAGT-AAAATATAATTTTTGGAAGTTTA
1 GGGTAAAAATGTAATTTTTGGAAGTTCA
*
21949496 GGG-ACAAAATGTAATTTTTAAGAAGTTCGA
1 GGGTA-AAAATGTAATTTTT-GGAAGTTC-A
*
21949526 GGG-AAAAATATAATTT
1 GGGTAAAAATGTAATTT
21949542 GTAAAAAGTT
Statistics
Matches: 136, Mismatches: 11, Indels: 22
0.80 0.07 0.13
Matches are distributed among these distances:
26 1 0.01
27 26 0.19
28 39 0.29
29 65 0.48
30 5 0.04
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (28 bp):
GGGTAAAAATGTAATTTTTGGAAGTTCA
Found at i:21949415 original size:58 final size:55
Alignment explanation
Indices: 21949353--21949528 Score: 151
Period size: 56 Copynumber: 3.1 Consensus size: 55
21949343 AAAAAGTTTT
21949353 AGGGGTAAAAATGTCATTTTAGGAAAATTCAGGGTA-AAAATGTGATTTTTGGAAGTTC
1 AGGGGTAAAAATGTCATTTTAGG-AAATTC-GGG-ACAAAATGT-ATTTTTGGAAGTTC
* * *
21949411 AGGGGTAAAAATGTGATTTTTGGAAGTTCGGGAGCAAAATGTATTTTTGGAAGTTC
1 AGGGGTAAAAATGTCATTTTAGGAAATTCGGGA-CAAAATGTATTTTTGGAAGTTC
* * * * * * *
21949467 -GAGAGT-AAAATATAATTTTTGGAAGTTTAGGGACAAAATGTAATTTTTAAGAAGTTC
1 AG-GGGTAAAAATGTCATTTTAGGAA-ATTCGGGACAAAATGT-ATTTTT-GGAAGTTC
21949524 GAGGG
1 -AGGG
21949529 AAAAATATAA
Statistics
Matches: 100, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
55 26 0.26
56 32 0.32
57 19 0.19
58 22 0.22
59 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (55 bp):
AGGGGTAAAAATGTCATTTTAGGAAATTCGGGACAAAATGTATTTTTGGAAGTTC
Found at i:21949541 original size:57 final size:56
Alignment explanation
Indices: 21949389--21949610 Score: 189
Period size: 58 Copynumber: 3.9 Consensus size: 56
21949379 ATTCAGGGTA
* * * * * *
21949389 AAAATGTGATTTTTGGAAGTTC-AGGGGTAAAAATGTGATTTTTGGAAG-TTCGGGAGC
1 AAAATGTAATTTTTAGAAGTTCGA-GGG-AAAAATATAATTTTTAGAAGTTTAGGGA-C
* * * *
21949446 AAAATGT-ATTTTTGGAAGTTCGAGAGTAAAATATAATTTTTGGAAGTTTAGGGAC
1 AAAATGTAATTTTTAGAAGTTCGAGGGAAAAATATAATTTTTAGAAGTTTAGGGAC
* * *
21949501 AAAATGTAATTTTTAAGAAGTTCGAGGGAAAAATATAATTTGTAAAAAGTTTAAGGGAA
1 AAAATGTAATTTTT-AGAAGTTCGAGGGAAAAATATAATTT-TTAGAAGTTT-AGGGAC
* * ** * *
21949560 AAAATGAAATTTTTAGAAATTTAAGGGCAAAATGTAATTTTTAAGAAGTTT
1 AAAATGTAATTTTTAGAAGTTCGAGGGAAAAATATAATTTTT-AGAAGTTT
21949611 GGAAGCAAAA
Statistics
Matches: 138, Mismatches: 20, Indels: 13
0.81 0.12 0.08
Matches are distributed among these distances:
55 25 0.18
56 28 0.20
57 32 0.23
58 35 0.25
59 18 0.13
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (56 bp):
AAAATGTAATTTTTAGAAGTTCGAGGGAAAAATATAATTTTTAGAAGTTTAGGGAC
Found at i:21949550 original size:29 final size:28
Alignment explanation
Indices: 21949460--21949609 Score: 97
Period size: 29 Copynumber: 5.2 Consensus size: 28
21949450 TGTATTTTTG
* * **
21949460 GAAGTTCGAGAGTAAAATATAATTTTTG
1 GAAGTTCGAGGGAAAAATATAATTTTAA
* *
21949488 GAAGTT-TAGGGACAAAATGTAATTTTTAA
1 GAAGTTCGAGGGA-AAAATATAA-TTTTAA
21949517 GAAGTTCGAGGGAAAAATATAATTTGTAA
1 GAAGTTCGAGGGAAAAATATAATTT-TAA
* ** *
21949546 AAAGTTTAAGGGAAAAA-ATGAAATTTTTA
1 GAAGTTCGAGGGAAAAATAT--AATTTTAA
* ** * *
21949575 GAAATTTAAGGGCAAAATGTAATTTTTAA
1 GAAGTTCGAGGGAAAAATATAA-TTTTAA
21949604 GAAGTT
1 GAAGTT
21949610 TGGAAGCAAA
Statistics
Matches: 96, Mismatches: 18, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
27 3 0.03
28 21 0.22
29 61 0.64
30 11 0.11
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.33
Consensus pattern (28 bp):
GAAGTTCGAGGGAAAAATATAATTTTAA
Found at i:21949618 original size:29 final size:28
Alignment explanation
Indices: 21949418--21949620 Score: 89
Period size: 28 Copynumber: 7.1 Consensus size: 28
21949408 TTCAGGGGTA
* * * *
21949418 AAAATGTGATTTTTGGAAGTTCGGGAGC
1 AAAATGTAATTTTTAGAAGTTTGGAAGC
* * *
21949446 AAAATGT-ATTTTTGGAAG-TTCGAGAGT
1 AAAATGTAATTTTTAGAAGTTTGGA-AGC
* * *
21949473 AAAATATAATTTTTGGAAGTTTAGGGA-C
1 AAAATGTAATTTTTAGAAGTTT-GGAAGC
* * *
21949501 AAAATGTAATTTTTAAGAAG-TTCGAGGGA
1 AAAATGTAATTTTT-AGAAGTTTGGA-AGC
* * *
21949530 AAAATATAATTTGTAAAAAGTTTAAGGGAA--
1 AAAATGTAATTT-TTAGAAGTTT---GGAAGC
* *
21949560 AAAATGAAATTTTTAGAAATTT--AAGGGC
1 AAAATGTAATTTTTAGAAGTTTGGAA--GC
21949588 AAAATGTAATTTTTAAGAAGTTTGGAAGC
1 AAAATGTAATTTTT-AGAAGTTTGGAAGC
21949617 AAAA
1 AAAA
21949621 ATATGATTTC
Statistics
Matches: 130, Mismatches: 26, Indels: 37
0.67 0.13 0.19
Matches are distributed among these distances:
24 2 0.02
26 2 0.02
27 20 0.15
28 46 0.35
29 42 0.32
30 14 0.11
31 2 0.02
33 2 0.02
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (28 bp):
AAAATGTAATTTTTAGAAGTTTGGAAGC
Found at i:21949645 original size:87 final size:87
Alignment explanation
Indices: 21949480--21949645 Score: 219
Period size: 87 Copynumber: 1.9 Consensus size: 87
21949470 AGTAAAATAT
* * * * *
21949480 AATTTTTGGAAGTTTAGGGACAAAATGTAATTTTTAAGAAGTTCGAGGGAAAAATATAATTTGTA
1 AATTTTTAGAAATTTAGGGACAAAATGTAATTTTTAAGAAGTTCGAAGCAAAAATATAATTTCTA
21949545 AAAAGTTTAAGGGAAAAAATGA
66 AAAAGTTTAAGGGAAAAAATGA
* *
21949567 AATTTTTAGAAATTTAAGGG-CAAAATGTAATTTTTAAGAAGTTTGGAAGCAAAAATATGATTTC
1 AATTTTTAGAAATTT-AGGGACAAAATGTAATTTTTAAGAAG-TTCGAAGCAAAAATATAATTTC
* *
21949631 TAGATAGTTT-AGGGA
64 TAAAAAGTTTAAGGGA
21949646 CCTTCTGGGC
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
87 39 0.57
88 29 0.43
ACGTcount: A:0.43, C:0.03, G:0.21, T:0.33
Consensus pattern (87 bp):
AATTTTTAGAAATTTAGGGACAAAATGTAATTTTTAAGAAGTTCGAAGCAAAAATATAATTTCTA
AAAAGTTTAAGGGAAAAAATGA
Found at i:21951460 original size:34 final size:32
Alignment explanation
Indices: 21951416--21951488 Score: 112
Period size: 34 Copynumber: 2.2 Consensus size: 32
21951406 TTAAAGTTTA
21951416 AATTT-AATTTAAAATAAATTCAAACTCAAAAT
1 AATTTAAATTTAAAATAAATTCAAACT-AAAAT
*
21951448 AAGTTTAAATTTAAAATAAATTCAAACTTAAAT
1 AA-TTTAAATTTAAAATAAATTCAAACTAAAAT
21951481 AATTTAAA
1 AATTTAAA
21951489 ATTGAGTTCT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
32 8 0.21
33 9 0.24
34 21 0.55
ACGTcount: A:0.56, C:0.07, G:0.01, T:0.36
Consensus pattern (32 bp):
AATTTAAATTTAAAATAAATTCAAACTAAAAT
Found at i:21951478 original size:17 final size:17
Alignment explanation
Indices: 21951424--21951479 Score: 76
Period size: 17 Copynumber: 3.3 Consensus size: 17
21951414 TAAATTTAAT
21951424 TTAAAATAAATTCAAAC
1 TTAAAATAAATTCAAAC
* * * *
21951441 TCAAAATAAGTTTAAAT
1 TTAAAATAAATTCAAAC
21951458 TTAAAATAAATTCAAAC
1 TTAAAATAAATTCAAAC
21951475 TTAAA
1 TTAAA
21951480 TAATTTAAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (17 bp):
TTAAAATAAATTCAAAC
Found at i:21951968 original size:39 final size:39
Alignment explanation
Indices: 21951909--21952636 Score: 328
Period size: 39 Copynumber: 18.7 Consensus size: 39
21951899 AATGATTGCA
* * * *
21951909 ATCTGCCCCATGATCAGGGTAAGAGATTGGCTGATGATG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGATG
* * * * * *
21951948 ATTTGCCCCAAGCTCGGGGTAAAAGATCGAATG--GCTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGATG
* * * *
21951985 CAATCTACCCCAGGCTCGGGGTAAGAAATTGGCTAATGATG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGATG
* * *
21952026 ATCTGCCCCAGGCTCGGGGTAAGAGATCGAATG--GCTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGATG
* *
21952063 CAATTTGCCCCAGGCTCGGGATAAGAGATTTG-CTGATGATG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGA-TTGACTGATGATG
* ** * * * ** * * *
21952104 AGT-AGCCTTAGGCTCGAGATAAGAAATCAAATGGTTG-TA
1 A-TCTGCCCCAGGCTCGGGGTAAGAGATTGACT-GATGATG
* * * *
21952143 ATCTGCCCTAAGCTCGGGGTAA-AGGATTTACTGATAATG
1 ATCTGCCCCAGGCTCGGGGTAAGA-GATTGACTGATGATG
* * * * * *
21952182 ATCTGTCTCAAGCTCGGGGTAAGAGATCGAATG--GCTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGATG
* * * * *
21952219 CAATCTGCCCTAAGCTCGGCGTAAGAGATTTG-CTGATAACG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGA-TTGACTGATGATG
* * * *
21952260 ATCTGCCCCAGGCTTGGGGTAAGAGATCGAATG--GCTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGATG
* *
21952297 CAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTAATGATG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGATG
* * * *
21952338 ATCTGCCCCAAGCTCGGGGTAAGAGATCGAATG--GTTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGATG
* * * *
21952375 CAATCTACCCTAAGCTCGGGGTAAGAGATTTACTGATGATG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGATG
* * * * ** * *
21952416 ATCTGCCTCAGTCTCAGAGTAAGAGATCAAATG--GTTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGATG
* * *
21952453 CAATCTACCCCAAGCTCGGGGTAAGAGATTTG-TTGATGATG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGA-TTGACTGATGATG
* * * * *
21952494 ATCTG-TCTAGGCTCGGGGTAAGAGATCGAATG--GTTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGATG
* * * * * * **
21952530 CAATCTGCCTCAGGATCGGGGTAAGAGATCGAATGGTTACA
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGATG
* *
21952571 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGATG
** **
21952610 ATCTATCTTAGGCTCGGGGTAAGAGAT
1 ATCTGCCCCAGGCTCGGGGTAAGAGAT
21952637 CGGATCTTCG
Statistics
Matches: 501, Mismatches: 147, Indels: 82
0.69 0.20 0.11
Matches are distributed among these distances:
36 3 0.01
37 17 0.03
38 31 0.06
39 424 0.85
40 10 0.02
41 16 0.03
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (39 bp):
ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGATG
Found at i:21952025 original size:78 final size:78
Alignment explanation
Indices: 21951896--21952558 Score: 749
Period size: 78 Copynumber: 8.5 Consensus size: 78
21951886 CTTTATCGCT
* * * * * *
21951896 TCGAATGATTGCAATCTGCCCCATGATCAGGGTAAGAGATTGGCTGATGATGATTTGCCCCAAGC
1 TCGAATGGTTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAAGC
*
21951961 TCGGGGTAAAAGA
66 TCGGGGTAAGAGA
* * * * * * *
21951974 TCGAATGGCTGCAATCTACCCCAGGCTCGGGGTAAGAAATTGGCTAATGATGATCTGCCCCAGGC
1 TCGAATGGTTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAAGC
21952039 TCGGGGTAAGAGA
66 TCGGGGTAAGAGA
* * * * * ** *
21952052 TCGAATGGCTGCAATTTGCCCCAGGCTCGGGATAAGAGATTTGCTGATGATGAGT-AGCCTTAGG
1 TCGAATGGTTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTTGCTGATGATGA-TCTGCCCCAAG
* * *
21952116 CTCGAGATAAGAAA
65 CTCGGGGTAAGAGA
* * * * * * *
21952130 TCAAATGGTTGTAATCTGCCCTAAGCTCGGGGTAA-AGGATTTACTGATAATGATCTGTCTCAAG
1 TCGAATGGTTGCAATCTGCCCCAAGCTCGGGGTAAGA-GATTTGCTGATGATGATCTGCCCCAAG
21952194 CTCGGGGTAAGAGA
65 CTCGGGGTAAGAGA
* * * * * *
21952208 TCGAATGGCTGCAATCTGCCCTAAGCTCGGCGTAAGAGATTTGCTGATAACGATCTGCCCCAGGC
1 TCGAATGGTTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAAGC
*
21952273 TTGGGGTAAGAGA
66 TCGGGGTAAGAGA
* * * *
21952286 TCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTAATGATGATCTGCCCCAAGC
1 TCGAATGGTTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAAGC
21952351 TCGGGGTAAGAGA
66 TCGGGGTAAGAGA
* * * *
21952364 TCGAATGGTTGCAATCTACCCTAAGCTCGGGGTAAGAGATTTACTGATGATGATCTGCCTC-AGT
1 TCGAATGGTTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAAG-
* *
21952428 CTCAGAGTAAGAGA
65 CTCGGGGTAAGAGA
* * * * * *
21952442 TCAAATGGTTGCAATCTACCCCAAGCTCGGGGTAAGAGATTTGTTGATGATGATCTG-TCTAGGC
1 TCGAATGGTTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAAGC
21952506 TCGGGGTAAGAGA
66 TCGGGGTAAGAGA
* * *
21952519 TCGAATGGTTGCAATCTGCCTCAGGATCGGGGTAAGAGAT
1 TCGAATGGTTGCAATCTGCCCCAAGCTCGGGGTAAGAGAT
21952559 CGAATGGTTA
Statistics
Matches: 496, Mismatches: 83, Indels: 13
0.84 0.14 0.02
Matches are distributed among these distances:
77 51 0.10
78 443 0.89
79 2 0.00
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (78 bp):
TCGAATGGTTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAAGC
TCGGGGTAAGAGA
Found at i:21962041 original size:97 final size:97
Alignment explanation
Indices: 21961870--21962063 Score: 316
Period size: 97 Copynumber: 2.0 Consensus size: 97
21961860 AACCTTGAAA
* *
21961870 AAGGGTACTCGATTATCCCGGTTTGAAGAAAAGTCGCGCCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGGTACTCGATTATCCCGATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCA
*
21961935 AAACTCGAAATAAAAGAATATTGCCTCGATTT
66 AAACCCGAAATAAAAGAATATTGCCTCGATTT
* * * *
21961967 AAGGGTATTTGATTATCCCGATTTGAAGAAAAATTGCGCCTAGTAAGTTAAGGCACGAATTTTCA
1 AAGGGTACTCGATTATCCCGATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCA
*
21962032 AAACCCGAAATAAAGGAATATTGCCTCGATTT
66 AAACCCGAAATAAAAGAATATTGCCTCGATTT
21962064 TAAATATTTT
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
97 89 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (97 bp):
AAGGGTACTCGATTATCCCGATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCA
AAACCCGAAATAAAAGAATATTGCCTCGATTT
Found at i:21962201 original size:14 final size:14
Alignment explanation
Indices: 21962182--21962222 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
21962172 AAGAATGAAC
21962182 AAATATACGAAAAT
1 AAATATACGAAAAT
21962196 AAATATGA-GAAAAAT
1 AAATAT-ACG-AAAAT
21962211 AAA-ATACGAAAA
1 AAATATACGAAAA
21962223 AATAAATAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 5 0.21
14 10 0.42
15 9 0.38
ACGTcount: A:0.68, C:0.05, G:0.10, T:0.17
Consensus pattern (14 bp):
AAATATACGAAAAT
Found at i:21962223 original size:14 final size:15
Alignment explanation
Indices: 21962182--21962230 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
21962172 AAGAATGAAC
21962182 AAATATACG-AAAAT
1 AAATATACGAAAAAT
21962196 AAATATGA-GAAAAAT
1 AAATAT-ACGAAAAAT
21962211 AAA-ATACGAAAAAAT
1 AAATATACG-AAAAAT
21962226 AAATA
1 AAATA
21962231 AGAAAATACT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
13 1 0.03
14 10 0.33
15 18 0.60
16 1 0.03
ACGTcount: A:0.69, C:0.04, G:0.08, T:0.18
Consensus pattern (15 bp):
AAATATACGAAAAAT
Found at i:21962235 original size:14 final size:14
Alignment explanation
Indices: 21962191--21962236 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
21962181 CAAATATACG
*
21962191 AAAATAAATATGAGA
1 AAAATAAATAAGA-A
*
21962206 AAAATAAAATACGAA
1 AAAAT-AAATAAGAA
21962221 AAAATAAATAAGAA
1 AAAATAAATAAGAA
21962235 AA
1 AA
21962237 TACTAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 10 0.36
15 11 0.39
16 7 0.25
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.15
Consensus pattern (14 bp):
AAAATAAATAAGAA
Found at i:21962456 original size:28 final size:29
Alignment explanation
Indices: 21962424--21962659 Score: 214
Period size: 28 Copynumber: 8.2 Consensus size: 29
21962414 GTTTATGGGT
* *
21962424 CAAAATGTGATTTTT-AGAAGTTCGAGAG
1 CAAAATGTAATTTTTGAGAAGTTCGAGGG
* * ** *
21962452 CAAAATATAATATTTG-GAAGTTCTTGGAT
1 CAAAATGTAATTTTTGAGAAGTTCGAGG-G
* * *
21962481 AAAAATGTAATTTTTGAGAAGTTCGAAAGT
1 CAAAATGTAATTTTTGAGAAGTTCG-AGGG
* *
21962511 CAAAATGTGATTTTTG-GAAGTT-TAGGGG
1 CAAAATGTAATTTTTGAGAAGTTCGA-GGG
*
21962539 CAAAAATGGAATTTTTGAGAAGTTCGAGGG
1 C-AAAATGTAATTTTTGAGAAGTTCGAGGG
*
21962569 CAAAAATGTAATTTTTGAGAAGTTTG-GGG
1 C-AAAATGTAATTTTTGAGAAGTTCGAGGG
*
21962598 TAAAATGTAATTTTTGA-AAGTTCGAGGG
1 CAAAATGTAATTTTTGAGAAGTTCGAGGG
* * *
21962626 TAAAATGTAATTTTTAAGAAGTTTGAGGG
1 CAAAATGTAATTTTTGAGAAGTTCGAGGG
*
21962655 TAAAA
1 CAAAA
21962660 ATATGATTTT
Statistics
Matches: 171, Mismatches: 27, Indels: 19
0.79 0.12 0.09
Matches are distributed among these distances:
27 7 0.04
28 57 0.33
29 50 0.29
30 55 0.32
31 2 0.01
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (29 bp):
CAAAATGTAATTTTTGAGAAGTTCGAGGG
Found at i:21962545 original size:116 final size:115
Alignment explanation
Indices: 21962396--21962671 Score: 321
Period size: 116 Copynumber: 2.4 Consensus size: 115
21962386 ATTCGAGGTA
* *
21962396 AAAACGTGATTTTTGGAAGTTTATGGGTC-AAAATGTGATTTTT-AGAAGTTCGAGAGC-AAAAT
1 AAAATGTGATTTTTGGAAGTTTA-GGGGCAAAAATGTGATTTTTGAGAAGTTCGAGAGCAAAAAT
*
21962458 ATAATATTTG-GAAGTTCTTGGATAAAAATGTAATTTTTGAGAAGTTCGAAAGT
65 ATAATATTTGAGAAGTT-TGGGAT-AAAATGTAATTTTTGA-AAGTTCGAAAGT
*
21962511 CAAAATGTGATTTTTGGAAGTTTAGGGGCAAAAATG-GAATTTTTGAGAAGTTCGAGGGCAAAAA
1 -AAAATGTGATTTTTGGAAGTTTAGGGGCAAAAATGTG-ATTTTTGAGAAGTTCGAGAGCAAAAA
* * * **
21962575 TGTAATTTTTGAGAAGTTTGGGGTAAAATGTAATTTTTGAAAGTTCGAGGGT
64 TATAATATTTGAGAAGTTTGGGATAAAATGTAATTTTTGAAAGTTCGAAAGT
* * * *
21962627 AAAATGTAATTTTTAAGAAGTTT-GAGGGTAAAAATATGATTTTTG
1 AAAATGTGATTTTT-GGAAGTTTAG-GGGCAAAAATGTGATTTTTG
21962672 GACTGTTTAG
Statistics
Matches: 139, Mismatches: 13, Indels: 16
0.83 0.08 0.10
Matches are distributed among these distances:
115 19 0.14
116 67 0.48
117 30 0.22
118 17 0.12
119 6 0.04
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.36
Consensus pattern (115 bp):
AAAATGTGATTTTTGGAAGTTTAGGGGCAAAAATGTGATTTTTGAGAAGTTCGAGAGCAAAAATA
TAATATTTGAGAAGTTTGGGATAAAATGTAATTTTTGAAAGTTCGAAAGT
Found at i:21962669 original size:29 final size:29
Alignment explanation
Indices: 21962387--21962659 Score: 222
Period size: 29 Copynumber: 9.4 Consensus size: 29
21962377 TTTAGGAAAA
* *
21962387 TTCGA-GGTAAAAACGTGATTTTTG-GAAG
1 TTCGAGGGT-AAAATGTAATTTTTGAGAAG
* *
21962415 TT-TATGGGTCAAAATGTGATTTTT-AGAAG
1 TTCGA-GGGT-AAAATGTAATTTTTGAGAAG
* * * *
21962444 TTCGAGAGCAAAATATAATATTTG-GAAG
1 TTCGAGGGTAAAATGTAATTTTTGAGAAG
** *
21962472 TTCTTGGATAAAAATGTAATTTTTGAGAAG
1 TTCGAGGGT-AAAATGTAATTTTTGAGAAG
** *
21962502 TTCGAAAGTCAAAATGTGATTTTTG-GAAG
1 TTCGAGGGT-AAAATGTAATTTTTGAGAAG
* * *
21962531 TT-TAGGGGCAAAAATGGAATTTTTGAGAAG
1 TTCGA-GGG-TAAAATGTAATTTTTGAGAAG
*
21962561 TTCGAGGGCAAAAATGTAATTTTTGAGAAG
1 TTCGAGGG-TAAAATGTAATTTTTGAGAAG
*
21962591 TTTG-GGGTAAAATGTAATTTTTGA-AAG
1 TTCGAGGGTAAAATGTAATTTTTGAGAAG
*
21962618 TTCGAGGGTAAAATGTAATTTTTAAGAAG
1 TTCGAGGGTAAAATGTAATTTTTGAGAAG
*
21962647 TTTGAGGGTAAAA
1 TTCGAGGGTAAAA
21962660 ATATGATTTT
Statistics
Matches: 196, Mismatches: 36, Indels: 25
0.76 0.14 0.10
Matches are distributed among these distances:
27 7 0.04
28 57 0.29
29 75 0.38
30 56 0.29
31 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.34
Consensus pattern (29 bp):
TTCGAGGGTAAAATGTAATTTTTGAGAAG
Found at i:21964501 original size:34 final size:32
Alignment explanation
Indices: 21964457--21964538 Score: 121
Period size: 34 Copynumber: 2.5 Consensus size: 32
21964447 TTAAAGTTTA
21964457 AATTT-AATTTAAAATAAATTCAAACTCAAAAT
1 AATTTAAATTTAAAATAAATTCAAACT-AAAAT
*
21964489 AAGTTTAAATTTAAAATAAATTCAAACTTAAAT
1 AA-TTTAAATTTAAAATAAATTCAAACTAAAAT
21964522 AATTTAAATTTTAAAAT
1 AATTTAAA-TTTAAAAT
21964539 TGAGTTTTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
32 8 0.17
33 17 0.37
34 21 0.46
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.38
Consensus pattern (32 bp):
AATTTAAATTTAAAATAAATTCAAACTAAAAT
Found at i:21964519 original size:17 final size:17
Alignment explanation
Indices: 21964465--21964520 Score: 76
Period size: 17 Copynumber: 3.3 Consensus size: 17
21964455 TAAATTTAAT
21964465 TTAAAATAAATTCAAAC
1 TTAAAATAAATTCAAAC
* * * *
21964482 TCAAAATAAGTTTAAAT
1 TTAAAATAAATTCAAAC
21964499 TTAAAATAAATTCAAAC
1 TTAAAATAAATTCAAAC
21964516 TTAAA
1 TTAAA
21964521 TAATTTAAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (17 bp):
TTAAAATAAATTCAAAC
Found at i:21964535 original size:16 final size:16
Alignment explanation
Indices: 21964485--21964536 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
21964475 TTCAAACTCA
*
21964485 AAATAAGTTTAAATTTA
1 AAATAA-TTTAAATTTT
* *
21964502 AAATAAATTCAAA-CTT
1 AAAT-AATTTAAATTTT
21964518 AAATAATTTAAATTTT
1 AAATAATTTAAATTTT
21964534 AAA
1 AAA
21964537 ATTGAGTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
15 7 0.25
16 10 0.36
17 9 0.32
18 2 0.07
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (16 bp):
AAATAATTTAAATTTT
Found at i:21964538 original size:17 final size:16
Alignment explanation
Indices: 21964457--21964538 Score: 69
Period size: 17 Copynumber: 5.0 Consensus size: 16
21964447 TTAAAGTTTA
21964457 AATTT-AATTTAAAAT
1 AATTTAAATTTAAAAT
* * *
21964472 AAATTCAAACTCAAAAT
1 -AATTTAAATTTAAAAT
21964489 AAGTTTAAATTTAAAAT
1 AA-TTTAAATTTAAAAT
* *
21964506 AAATTCAAACTT-AAAT
1 -AATTTAAATTTAAAAT
21964522 AATTTAAATTTTAAAAT
1 AATTTAAA-TTTAAAAT
21964539 TGAGTTTTAT
Statistics
Matches: 51, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
15 7 0.14
16 12 0.24
17 30 0.59
18 2 0.04
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.38
Consensus pattern (16 bp):
AATTTAAATTTAAAAT
Found at i:21969589 original size:20 final size:20
Alignment explanation
Indices: 21969566--21969604 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
21969556 TATTTGGGTC
21969566 TCACAG-ATTTTATTATCTTG
1 TCACAGTATTTTATT-TCTTG
*
21969586 TCACTGTATTTTATTTCTT
1 TCACAGTATTTTATTTCTT
21969605 TAACAGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.21, C:0.15, G:0.08, T:0.56
Consensus pattern (20 bp):
TCACAGTATTTTATTTCTTG
Found at i:21970484 original size:32 final size:33
Alignment explanation
Indices: 21970426--21970493 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 33
21970416 AAATTTTAAT
* *
21970426 AAATAAAAAAATTATTAAATTATT-AAATATTA
1 AAATAAAAAAATTATAAAATTATTAAAAAATTA
* *
21970458 AAATAAAATAA-TATAAATATTTTTAAAAAATTA
1 AAATAAAAAAATTATAAA-ATTATTAAAAAATTA
21970491 AAA
1 AAA
21970494 ATTAATATGG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
31 5 0.17
32 15 0.50
33 10 0.33
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (33 bp):
AAATAAAAAAATTATAAAATTATTAAAAAATTA
Found at i:21974760 original size:16 final size:16
Alignment explanation
Indices: 21974739--21974777 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
21974729 TCTAGGTTGA
21974739 TTAATTGAATTTTCTT
1 TTAATTGAATTTTCTT
21974755 TTAATTGAATTTTCTT
1 TTAATTGAATTTTCTT
21974771 TCTAATT
1 T-TAATT
21974778 AAAACCCCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.62
Consensus pattern (16 bp):
TTAATTGAATTTTCTT
Found at i:21977119 original size:15 final size:16
Alignment explanation
Indices: 21977077--21977121 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
21977067 TGACAATATA
21977077 TTTCTTTTCTTTTCTCT
1 TTTCTTTT-TTTTCTCT
21977094 TTTCTTCTTTTTTCT-T
1 TTTCTT-TTTTTTCTCT
*
21977110 TTTGTTTTTTTT
1 TTTCTTTTTTTT
21977122 GTGATTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 6 0.23
16 6 0.23
17 12 0.46
18 2 0.08
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (16 bp):
TTTCTTTTTTTTCTCT
Found at i:21988451 original size:17 final size:17
Alignment explanation
Indices: 21988424--21988462 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
21988414 TTTTGTCTTT
21988424 TTTTTTCTCAATTTTCTC
1 TTTTTTCTCAATTTT-TC
21988442 TTTTTT-TCAATTTTTC
1 TTTTTTCTCAATTTTTC
21988458 TTTTT
1 TTTTT
21988463 GACTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.33
17 8 0.38
18 6 0.29
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTTCTCAATTTTTC
Found at i:21989405 original size:6 final size:6
Alignment explanation
Indices: 21989396--21989439 Score: 79
Period size: 6 Copynumber: 7.3 Consensus size: 6
21989386 AGTGCATAAT
*
21989396 AAAATA AAAATA AAAATA AAAATA AAACTA AAAATA AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AA
21989440 TGTACTAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.82, C:0.02, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:21989468 original size:7 final size:8
Alignment explanation
Indices: 21989449--21989477 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
21989439 ATGTACTAAT
21989449 TTTTTGAA
1 TTTTTGAA
21989457 TTTTTGAA
1 TTTTTGAA
21989465 TTTTTGAA
1 TTTTTGAA
21989473 TTTTT
1 TTTTT
21989478 ATTTCAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (8 bp):
TTTTTGAA
Found at i:21991089 original size:25 final size:25
Alignment explanation
Indices: 21991055--21991102 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
21991045 TTTTAGAAGA
21991055 AATAAAGAGTACAACGAAACTTACT
1 AATAAAGAGTACAACGAAACTTACT
*
21991080 AATAAAGAGTACAACGAAGCTTA
1 AATAAAGAGTACAACGAAACTTA
21991103 GTATCTCTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.52, C:0.15, G:0.15, T:0.19
Consensus pattern (25 bp):
AATAAAGAGTACAACGAAACTTACT
Found at i:21992724 original size:17 final size:18
Alignment explanation
Indices: 21992687--21992726 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
21992677 TAACAAAATG
*
21992687 ATGCGATGATAAAATAAA
1 ATGCAATGATAAAATAAA
*
21992705 ATGCAATGATAATA-AAA
1 ATGCAATGATAAAATAAA
21992722 ATGCA
1 ATGCA
21992727 TTAAAACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.55, C:0.07, G:0.15, T:0.23
Consensus pattern (18 bp):
ATGCAATGATAAAATAAA
Found at i:21994625 original size:12 final size:12
Alignment explanation
Indices: 21994604--21994632 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
21994594 GAGATTAAAG
21994604 TTTT-GGAGTGT
1 TTTTGGGAGTGT
21994615 TTTTGGGAGTGT
1 TTTTGGGAGTGT
21994627 TTTTGG
1 TTTTGG
21994633 ATGCACGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.07, C:0.00, G:0.38, T:0.55
Consensus pattern (12 bp):
TTTTGGGAGTGT
Found at i:21995054 original size:15 final size:16
Alignment explanation
Indices: 21995026--21995055 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
21995016 ACAACACGAC
21995026 GAAAAGTGAAATAAAT
1 GAAAAGTGAAATAAAT
21995042 GAAAAGT-AAATAAA
1 GAAAAGTGAAATAAA
21995056 AAAATTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (16 bp):
GAAAAGTGAAATAAAT
Found at i:22003603 original size:48 final size:46
Alignment explanation
Indices: 22003551--22003640 Score: 110
Period size: 48 Copynumber: 1.9 Consensus size: 46
22003541 AAATTCAATT
*
22003551 AAAAACAA-AAAAATATGAAAATAAAAATAAAAATGGCTAAATAAAGGG
1 AAAAA-AATAAAAATATAAAAATAAAAATAAAAAT-GC-AAATAAAGGG
* * *
22003599 AAAAAAATTAAAATATAAAAATTAAATTAAAAATGCAAATAA
1 AAAAAAATAAAAATATAAAAATAAAAATAAAAATGCAAATAA
22003641 TAAAACAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
46 6 0.16
47 4 0.11
48 27 0.73
ACGTcount: A:0.70, C:0.03, G:0.08, T:0.19
Consensus pattern (46 bp):
AAAAAAATAAAAATATAAAAATAAAAATAAAAATGCAAATAAAGGG
Found at i:22003664 original size:75 final size:75
Alignment explanation
Indices: 22003524--22003666 Score: 182
Period size: 76 Copynumber: 1.9 Consensus size: 75
22003514 ACCTATAAAT
* * *
22003524 AAAAAAATTAAATGTAAAAATTCAATTAAAAACAAAAAAATATGAAAATAAAAATAAAAATGGCT
1 AAAAAAATTAAATATAAAAATTAAATTAAAAACAAAAAAATATGAAAACAAAAATAAAAATGGCT
22003589 AAATAAAGGG
66 AAATAAAGGG
*** * *
22003599 AAAAAAATTAAAATATAAAAATTAAATTAAAAATGCAAATA-AT-AAAACAAAATTAAAAAATGG
1 AAAAAAATT-AAATATAAAAATTAAATTAAAAACAAAAAAATATGAAAACAAAAAT-AAAAATGG
22003662 CTAAA
64 CTAAA
22003667 GTAATAGAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
74 9 0.16
75 24 0.41
76 25 0.43
ACGTcount: A:0.68, C:0.04, G:0.07, T:0.21
Consensus pattern (75 bp):
AAAAAAATTAAATATAAAAATTAAATTAAAAACAAAAAAATATGAAAACAAAAATAAAAATGGCT
AAATAAAGGG
Found at i:22011119 original size:25 final size:24
Alignment explanation
Indices: 22011081--22011128 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
22011071 ATTAATATAA
22011081 AATTATTTTATTTAATACTAATAC
1 AATTATTTTATTTAATACTAATAC
*
22011105 AATTATTTTTATTTAATATTAATA
1 AATTA-TTTTATTTAATACTAATA
22011129 TTAATATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (24 bp):
AATTATTTTATTTAATACTAATAC
Found at i:22012706 original size:14 final size:15
Alignment explanation
Indices: 22012681--22012709 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
22012671 TTGAGGTAAT
22012681 AAATATATAATATTA
1 AAATATATAATATTA
22012696 AAATATA-AATATTA
1 AAATATATAATATTA
22012710 TATTAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATATATAATATTA
Found at i:22012707 original size:19 final size:18
Alignment explanation
Indices: 22012678--22012723 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
22012668 TAATTGAGGT
22012678 AATAAATATATAATATTAA
1 AATAAA-ATATAATATTAA
*
22012697 AATATAAATATTATATTAA
1 AATA-AAATATAATATTAA
22012716 AATAAAAT
1 AATAAAAT
22012724 TTTGGTTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 4 0.16
19 19 0.76
20 2 0.08
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AATAAAATATAATATTAA
Found at i:22014371 original size:6 final size:6
Alignment explanation
Indices: 22014360--22014387 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
22014350 TAGTAGCATG
22014360 GAAAAT GAAAAT GAAAAT GAAAAT GAAA
1 GAAAAT GAAAAT GAAAAT GAAAAT GAAA
22014388 CAGGAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.18, T:0.14
Consensus pattern (6 bp):
GAAAAT
Found at i:22020084 original size:64 final size:63
Alignment explanation
Indices: 22019940--22020068 Score: 170
Period size: 64 Copynumber: 2.0 Consensus size: 63
22019930 CCTGGAAAAA
* * *
22019940 AGAAAAAAAATGAGAGAAAATGGGTGTTTGGAAAGAGAGAAAGTTCGAGAAAATGAGAAAATCT
1 AGAAAAAGAA-GAGAGAAAATGGGTGTTTGGAAAGAGAGAAAGTTCGAGAAAATAAGAAAATAT
*
22020004 AGAAAAATAATGAGAGAAAATGGGTGTTTGGAAAGAGAGAAAGTAT-GAGAAAATTTAAGAAAAT
1 AGAAAAAGAA-GAGAGAAAATGGGTGTTTGGAAAGAGAGAAAGT-TCGAGAAAA--TAAGAAAAT
22020068 A
62 A
22020069 ATTGGAAGGG
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
64 50 0.85
65 1 0.02
66 8 0.14
ACGTcount: A:0.53, C:0.02, G:0.27, T:0.19
Consensus pattern (63 bp):
AGAAAAAGAAGAGAGAAAATGGGTGTTTGGAAAGAGAGAAAGTTCGAGAAAATAAGAAAATAT
Found at i:22047432 original size:11 final size:11
Alignment explanation
Indices: 22047418--22047473 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
22047408 ATCGCATTCC
*
22047418 CATTGTCATTA
1 CATTGTCATTT
* *
22047429 CATTTTAATTGT
1 CATTGTCATT-T
22047441 CATTG-CATTT
1 CATTGTCATTT
22047451 GCATTGTCATTT
1 -CATTGTCATTT
*
22047463 CATTTTCATTT
1 CATTGTCATTT
22047474 GTCATGGTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
10 1 0.03
11 26 0.72
12 9 0.25
ACGTcount: A:0.21, C:0.16, G:0.09, T:0.54
Consensus pattern (11 bp):
CATTGTCATTT
Found at i:22047432 original size:17 final size:17
Alignment explanation
Indices: 22047401--22047478 Score: 75
Period size: 17 Copynumber: 4.5 Consensus size: 17
22047391 TGTTAGTAAG
* *
22047401 CATTGTCATCGCATTCC
1 CATTGTCATTGCATTTC
* *
22047418 CATTGTCATTACATTTT
1 CATTGTCATTGCATTTC
* *
22047435 AATTGTCATTGCATTTG
1 CATTGTCATTGCATTTC
* *
22047452 CATTGTCATTTCATTTT
1 CATTGTCATTGCATTTC
22047469 CATTTGTCAT
1 CA-TTGTCAT
22047479 GGTATTTTAG
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
17 43 0.86
18 7 0.14
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.49
Consensus pattern (17 bp):
CATTGTCATTGCATTTC
Found at i:22047449 original size:34 final size:35
Alignment explanation
Indices: 22047402--22047478 Score: 102
Period size: 34 Copynumber: 2.2 Consensus size: 35
22047392 GTTAGTAAGC
22047402 ATTGTCATCGCATTCCCATTGTCATTACATTTT-A
1 ATTGTCATCGCATTCCCATTGTCATTACATTTTCA
* ** *
22047436 ATTGTCATTGCATTTGCATTGTCATTTCATTTTCA
1 ATTGTCATCGCATTCCCATTGTCATTACATTTTCA
*
22047471 TTTGTCAT
1 ATTGTCAT
22047479 GGTATTTTAG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
34 29 0.78
35 8 0.22
ACGTcount: A:0.21, C:0.19, G:0.10, T:0.49
Consensus pattern (35 bp):
ATTGTCATCGCATTCCCATTGTCATTACATTTTCA
Found at i:22048538 original size:26 final size:26
Alignment explanation
Indices: 22048509--22048573 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
22048499 GCTGTATAAG
*
22048509 CATGTCCAGAATTATCGCTGCATGAA
1 CATGTCCAGAATTACCGCTGCATGAA
* *
22048535 CATGTCCAGAATTACCGTTGCATGAG
1 CATGTCCAGAATTACCGCTGCATGAA
* *
22048561 CACGTCCAAAATT
1 CATGTCCAGAATT
22048574 GCATCCAGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (26 bp):
CATGTCCAGAATTACCGCTGCATGAA
Found at i:22055019 original size:22 final size:22
Alignment explanation
Indices: 22054963--22055073 Score: 116
Period size: 22 Copynumber: 5.0 Consensus size: 22
22054953 GCTTACTGTT
22054963 TTGCACT-TCGTGTGCCTACTGA
1 TTGCACTAT-GTGTGCCTACTGA
** *
22054985 TTTGTGCTATGTGCGCCTACTGA
1 -TTGCACTATGTGTGCCTACTGA
*
22055008 TTGCACTATGTGCGCCTACTGA
1 TTGCACTATGTGTGCCTACTGA
* *
22055030 TTGCCCTGTGTGTGCCTACTGGA
1 TTGCACTATGTGTGCCTACT-GA
* *
22055053 TTGCACTGTGTGTGCTTACTG
1 TTGCACTATGTGTGCCTACTG
22055074 TTTCCCCAGC
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
22 38 0.50
23 37 0.49
24 1 0.01
ACGTcount: A:0.13, C:0.24, G:0.26, T:0.37
Consensus pattern (22 bp):
TTGCACTATGTGTGCCTACTGA
Found at i:22055025 original size:45 final size:44
Alignment explanation
Indices: 22054963--22055073 Score: 125
Period size: 45 Copynumber: 2.5 Consensus size: 44
22054953 GCTTACTGTT
**
22054963 TTGCACTTCGTGTGCCTACTGATTTGTGCTATGTGCGCCTACT-GA
1 TTGCACTT-GTGTGCCTACTGA-TTGCCCTATGTGCGCCTACTGGA
* * *
22055008 TTGCACTATGTGCGCCTACTGATTGCCCTGTGTGTGCCTACTGGA
1 TTGCACT-TGTGTGCCTACTGATTGCCCTATGTGCGCCTACTGGA
*
22055053 TTGCACTGTGTGTGCTTACTG
1 TTGCACT-TGTGTGCCTACTG
22055074 TTTCCCCAGC
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
44 16 0.29
45 39 0.70
46 1 0.02
ACGTcount: A:0.13, C:0.24, G:0.26, T:0.37
Consensus pattern (44 bp):
TTGCACTTGTGTGCCTACTGATTGCCCTATGTGCGCCTACTGGA
Found at i:22069119 original size:5 final size:5
Alignment explanation
Indices: 22069109--22069148 Score: 80
Period size: 5 Copynumber: 8.0 Consensus size: 5
22069099 TATTTTTCAG
22069109 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT
22069149 CCAAACAGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTCTT
Found at i:22074442 original size:21 final size:21
Alignment explanation
Indices: 22074410--22074461 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
22074400 GGAGTTTTTA
*
22074410 GTATCAGTAGAAG-CATGACAT
1 GTATCGGTAGAAGTCAT-ACAT
* *
22074431 GTTTCGGTAGAAGTCATACTT
1 GTATCGGTAGAAGTCATACAT
22074452 GTATCGGTAG
1 GTATCGGTAG
22074462 TATTGTCTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAAGTCATACAT
Found at i:22076113 original size:24 final size:24
Alignment explanation
Indices: 22076081--22076149 Score: 120
Period size: 24 Copynumber: 2.9 Consensus size: 24
22076071 GTGGAACCAA
*
22076081 TAGAAAATGAAGATCCAACTCAAG
1 TAGAAAATGAAGATCTAACTCAAG
*
22076105 TAGAAAATGAAGATCTAACTCCAG
1 TAGAAAATGAAGATCTAACTCAAG
22076129 TAGAAAATGAAGATCTAACTC
1 TAGAAAATGAAGATCTAACTC
22076150 TGTGTATGGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.20
Consensus pattern (24 bp):
TAGAAAATGAAGATCTAACTCAAG
Found at i:22079830 original size:43 final size:43
Alignment explanation
Indices: 22079766--22079862 Score: 149
Period size: 43 Copynumber: 2.3 Consensus size: 43
22079756 AACTTCACAA
* * *
22079766 TTAATGACATGTCACGATATTAACAAGAGTCAAGTAATATAAT
1 TTAATAACATGCCACGATATTAACAAGAGCCAAGTAATATAAT
* *
22079809 TTAATAACATGCCACGTTATTAACACGAGCCAAGTAATATAAT
1 TTAATAACATGCCACGATATTAACAAGAGCCAAGTAATATAAT
22079852 TTAATAACATG
1 TTAATAACATG
22079863 TCAATGAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.30
Consensus pattern (43 bp):
TTAATAACATGCCACGATATTAACAAGAGCCAAGTAATATAAT
Found at i:22079963 original size:27 final size:27
Alignment explanation
Indices: 22079923--22079977 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
22079913 TATATGGGAA
* *
22079923 TGGTATATTGCCTTCTGATTTCGGTAT
1 TGGTATATTACCTTCTGATTCCGGTAT
22079950 TGGTATATTACCTTCTGATTCCGGTAT
1 TGGTATATTACCTTCTGATTCCGGTAT
22079977 T
1 T
22079978 TATTTTCCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.16, C:0.16, G:0.20, T:0.47
Consensus pattern (27 bp):
TGGTATATTACCTTCTGATTCCGGTAT
Found at i:22081270 original size:28 final size:28
Alignment explanation
Indices: 22081236--22081295 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
22081226 ATTAATTAAT
*
22081236 ATTACTTACTTACTACTAACAAAATAAA
1 ATTACTTACTAACTACTAACAAAATAAA
*
22081264 ATTACTTACTAACTACTAACAAAATTAA
1 ATTACTTACTAACTACTAACAAAATAAA
22081292 ATTA
1 ATTA
22081296 AATTAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (28 bp):
ATTACTTACTAACTACTAACAAAATAAA
Found at i:22081406 original size:24 final size:23
Alignment explanation
Indices: 22081360--22081408 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
22081350 TACTAAATAA
*
22081360 AAAAATTAAATAACAAATCAAAT
1 AAAAATTAAATAACAAATAAAAT
22081383 AAAAATTAAACTAAACAAA-AAAAT
1 AAAAATTAAA-T-AACAAATAAAAT
22081407 AA
1 AA
22081409 CTTAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 10 0.43
24 7 0.30
25 6 0.26
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.18
Consensus pattern (23 bp):
AAAAATTAAATAACAAATAAAAT
Found at i:22081681 original size:12 final size:12
Alignment explanation
Indices: 22081664--22081745 Score: 87
Period size: 12 Copynumber: 6.8 Consensus size: 12
22081654 AAATAATCTT
22081664 CTTC-TTCTTCTC
1 CTTCTTTCTT-TC
22081676 CTTCTTTCTTTC
1 CTTCTTTCTTTC
* *
22081688 TTTCTTTTCTCTC
1 CTTC-TTTCTTTC
22081701 CTTC-TTCTTTC
1 CTTCTTTCTTTC
*
22081712 TTTCTTTCTTTC
1 CTTCTTTCTTTC
*
22081724 TTTCTTTCTTTC
1 CTTCTTTCTTTC
*
22081736 TTTCTTTCTT
1 CTTCTTTCTT
22081746 CTTCTTCTCT
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
11 9 0.15
12 38 0.61
13 15 0.24
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (12 bp):
CTTCTTTCTTTC
Found at i:22081686 original size:4 final size:4
Alignment explanation
Indices: 22081677--22081745 Score: 104
Period size: 4 Copynumber: 17.2 Consensus size: 4
22081667 CTTCTTCTCC
* *
22081677 TTCT TTCT TTCT TTCTT TTCT CTCC TTC- TTCT TTCT TTCT TTCT TTCT
1 TTCT TTCT TTCT TTC-T TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
22081725 TTCT TTCT TTCT TTCT TTCT T
1 TTCT TTCT TTCT TTCT TTCT T
22081746 CTTCTTCTCT
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
3 3 0.05
4 53 0.88
5 4 0.07
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
TTCT
Found at i:22081708 original size:20 final size:19
Alignment explanation
Indices: 22081662--22081748 Score: 104
Period size: 20 Copynumber: 4.4 Consensus size: 19
22081652 TAAAATAATC
*
22081662 TTCTTC-TTCTTCTCCTTCT
1 TTCTTCTTTCTT-TCTTTCT
* *
22081681 TTCTTTCTTTCTTTTCTCTCC
1 TTC-TTCTTTC-TTTCTTTCT
22081702 TTCTTCTTTCTTTCTTTCT
1 TTCTTCTTTCTTTCTTTCT
22081721 TTCTTTCTTTCTTTCTTTCT
1 TTC-TTCTTTCTTTCTTTCT
22081741 TTCTTCTT
1 TTCTTCTT
22081749 CTTCTCTCCC
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
19 18 0.31
20 29 0.49
21 10 0.17
22 2 0.03
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
TTCTTCTTTCTTTCTTTCT
Found at i:22081713 original size:28 final size:28
Alignment explanation
Indices: 22081676--22081757 Score: 114
Period size: 28 Copynumber: 2.9 Consensus size: 28
22081666 TCTTCTTCTC
22081676 CTTCTTTCTTTCTTTCTTTTCTCTCCTT
1 CTTCTTTCTTTCTTTCTTTTCTCTCCTT
* *
22081704 CTTCTTTCTTTCTTTC-TTTCTTTCTTT
1 CTTCTTTCTTTCTTTCTTTTCTCTCCTT
22081731 CTTTCTTTCTTTC-TTCTTCTTCTCTCC
1 C-TTCTTTCTTTCTTTCTT-TTCTCTCC
22081758 CGTTGGTCCC
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
27 13 0.28
28 28 0.60
29 6 0.13
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (28 bp):
CTTCTTTCTTTCTTTCTTTTCTCTCCTT
Found at i:22082001 original size:12 final size:12
Alignment explanation
Indices: 22081984--22082008 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
22081974 GTACTTTGCC
22081984 CGTGTATTTTGT
1 CGTGTATTTTGT
22081996 CGTGTATTTTGT
1 CGTGTATTTTGT
22082008 C
1 C
22082009 CATATTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.12, G:0.24, T:0.56
Consensus pattern (12 bp):
CGTGTATTTTGT
Found at i:22090620 original size:21 final size:21
Alignment explanation
Indices: 22090596--22090635 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
22090586 TGTGTCTGAT
22090596 TTTAGTATGGATGCATCTGGC
1 TTTAGTATGGATGCATCTGGC
* *
22090617 TTTATTGTGGATGCATCTG
1 TTTAGTATGGATGCATCTG
22090636 AGTGTGCTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.12, G:0.28, T:0.42
Consensus pattern (21 bp):
TTTAGTATGGATGCATCTGGC
Found at i:22092914 original size:105 final size:105
Alignment explanation
Indices: 22092729--22092947 Score: 402
Period size: 105 Copynumber: 2.1 Consensus size: 105
22092719 AATTAGGATT
* *
22092729 CAAAAGAACTAAATGATACAAAAATCAGAATGTGTATAAAAAGATCTAAAAGAACTTCTATTTTA
1 CAAAAGAACTAAATGATACAAAAATCAGAATGTGTATAAAAACATCCAAAAGAACTTCTATTTTA
*
22092794 TTAAATGATATAATATAAAAAGAATGTGTACAAAAATATC
66 TTAAATGATACAATATAAAAAGAATGTGTACAAAAATATC
*
22092834 CAAAAGAACTAAATGATACAAAAATTAGAATGTGTATAAAAACATCCAAAAGAACTTCTATTTTA
1 CAAAAGAACTAAATGATACAAAAATCAGAATGTGTATAAAAACATCCAAAAGAACTTCTATTTTA
22092899 TTAAATGATACAATATAAAAAGAATGTGTACAAAAATATC
66 TTAAATGATACAATATAAAAAGAATGTGTACAAAAATATC
22092939 CAAAAGAAC
1 CAAAAGAAC
22092948 ATCAATACAT
Statistics
Matches: 110, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 110 1.00
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.26
Consensus pattern (105 bp):
CAAAAGAACTAAATGATACAAAAATCAGAATGTGTATAAAAACATCCAAAAGAACTTCTATTTTA
TTAAATGATACAATATAAAAAGAATGTGTACAAAAATATC
Found at i:22093081 original size:33 final size:33
Alignment explanation
Indices: 22093019--22093081 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
22093009 GTTCCTTATT
** * *
22093019 GGTTCAGCTTTTGAACGGGGTTGTGGTTGTTAG
1 GGTTCAGCTTCCGAACGGGGTTATAGTTGTTAG
*
22093052 GGTTCAGCTTCCGAGCGGGGTTATAGTTGT
1 GGTTCAGCTTCCGAACGGGGTTATAGTTGT
22093082 GGTTGTTGGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.13, C:0.13, G:0.38, T:0.37
Consensus pattern (33 bp):
GGTTCAGCTTCCGAACGGGGTTATAGTTGTTAG
Found at i:22104546 original size:12 final size:12
Alignment explanation
Indices: 22104529--22104553 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
22104519 TGCTATTATG
22104529 ATGAATGCTATT
1 ATGAATGCTATT
22104541 ATGAATGCTATT
1 ATGAATGCTATT
22104553 A
1 A
22104554 ATTATTGATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
ATGAATGCTATT
Found at i:22109024 original size:15 final size:15
Alignment explanation
Indices: 22109004--22109038 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
22108994 AACCATTAAG
22109004 ACCAAACCCAATTGA
1 ACCAAACCCAATTGA
*
22109019 ACCAAACCTAATTGA
1 ACCAAACCCAATTGA
22109034 ACCAA
1 ACCAA
22109039 GTCCAAACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.49, C:0.31, G:0.06, T:0.14
Consensus pattern (15 bp):
ACCAAACCCAATTGA
Found at i:22111394 original size:12 final size:12
Alignment explanation
Indices: 22111377--22111406 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
22111367 GAGAGTTTGG
22111377 AGGCTCGTACTA
1 AGGCTCGTACTA
22111389 AGGCTCGTACTA
1 AGGCTCGTACTA
22111401 AGGCTC
1 AGGCTC
22111407 AGAGGGTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.27, G:0.27, T:0.23
Consensus pattern (12 bp):
AGGCTCGTACTA
Found at i:22115740 original size:15 final size:15
Alignment explanation
Indices: 22115720--22115757 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
22115710 CATTAAGCCG
22115720 AAATCCAATTGAACC
1 AAATCCAATTGAACC
22115735 AAATCCAATTGAACC
1 AAATCCAATTGAACC
*
22115750 AAGTCCAA
1 AAATCCAA
22115758 ACCCAAACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.47, C:0.26, G:0.08, T:0.18
Consensus pattern (15 bp):
AAATCCAATTGAACC
Found at i:22115802 original size:13 final size:13
Alignment explanation
Indices: 22115784--22115836 Score: 70
Period size: 13 Copynumber: 4.0 Consensus size: 13
22115774 ACCATTAACC
22115784 GACCGTTGACTTT
1 GACCGTTGACTTT
*
22115797 GACCGTTGACCGTT
1 GACCGTTGA-CTTT
*
22115811 GATCGTTGACTTT
1 GACCGTTGACTTT
*
22115824 GATCGTTGACTTT
1 GACCGTTGACTTT
22115837 TTTCGAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
13 25 0.69
14 11 0.31
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.40
Consensus pattern (13 bp):
GACCGTTGACTTT
Found at i:22115807 original size:7 final size:7
Alignment explanation
Indices: 22115784--22115833 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
22115774 ACCATTAACC
22115784 GACCGTT
1 GACCGTT
*
22115791 GA-CTTT
1 GACCGTT
22115797 GACCGTT
1 GACCGTT
22115804 GACCGTT
1 GACCGTT
*
22115811 GATCGTT
1 GACCGTT
*
22115818 GA-CTTT
1 GACCGTT
*
22115824 GATCGTT
1 GACCGTT
22115831 GAC
1 GAC
22115834 TTTTTTCGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
6 10 0.29
7 25 0.71
ACGTcount: A:0.16, C:0.22, G:0.26, T:0.36
Consensus pattern (7 bp):
GACCGTT
Found at i:22116905 original size:22 final size:24
Alignment explanation
Indices: 22116880--22116925 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
22116870 TACAAATTTA
22116880 TATTATTTT-ATTTT-ATTATTAT
1 TATTATTTTGATTTTGATTATTAT
22116902 TATTATTTTGATTTTGGATTATTA
1 TATTATTTTGATTTT-GATTATTA
22116926 ATTTACTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.43
23 5 0.24
25 7 0.33
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (24 bp):
TATTATTTTGATTTTGATTATTAT
Found at i:22122060 original size:328 final size:328
Alignment explanation
Indices: 22121463--22122117 Score: 1159
Period size: 328 Copynumber: 2.0 Consensus size: 328
22121453 ATGTTATGAC
* * * * *
22121463 TGGTATATTCTATCTTTTTTATGTAATTGTGTGTGCTTTGATTGACTCAAGGTCGACTCATTCTT
1 TGGTATATTCTATCTCTATGATGTAATTGTGTATGCTTTGATTGACTCAAGGTCAACTCATTCTT
*
22121528 ATATCTATACTACTTTAGCAACTGATAAAAATTTATCTGTCGAGTCAACTGAATTTAATATGCTA
66 ATATCTATACTACTTTAGCAACTGACAAAAATTTATCTGTCGAGTCAACTGAATTTAATATGCTA
** *
22121593 GTCACAAATTCGTTGGGTCATAGTGTTATAATAATTTTGATGTGCCATAAATGTTCACTGAAAGT
131 GTCACAAACCCGTTGGGTCATAGTGTTATAATAATTTTGATGTGCCATAAATGTTCACTAAAAGT
*
22121658 TCAAGGTTGCGAATTTCCTGCTGATATGATGTTACTAACTTTTTGTGAGTTCGATGTGATTCTAG
196 TCAAGGCTGCGAATTTCCTGCTGATATGATGTTACTAACTTTTTGTGAGTTCGATGTGATTCTAG
* *
22121723 GCATGGCTTGGTTATCTGAGCACGATGCGGAAGTAAACTGCAAGAAGAGACAAATTGATTTAAAA
261 ACATGGCTTGGTTATCTGAGCACGATGCAGAAGTAAACTGCAAGAAGAGACAAATTGATTTAAAA
22121788 TGT
326 TGT
*
22121791 TGGTATATTCTATCTCTATGATGTAATTGTGTATGCTTTGATTGACTC-TGGTTCAACTCATTCT
1 TGGTATATTCTATCTCTATGATGTAATTGTGTATGCTTTGATTGACTCAAGG-TCAACTCATTCT
*
22121855 TATATCTATACTACTTTAGCAACTGACAAAAATTTGTCTGTCGAGTCAACTGAATTTAATATGCT
65 TATATCTATACTACTTTAGCAACTGACAAAAATTTATCTGTCGAGTCAACTGAATTTAATATGCT
22121920 AGTCACAAACCCGTTGGGTCATAGTGTTATAATAATTTTGATGTGCCATAAATGTTCACTAAAAG
130 AGTCACAAACCCGTTGGGTCATAGTGTTATAATAATTTTGATGTGCCATAAATGTTCACTAAAAG
22121985 TTCAAGGCTGCGAATTTCCTGCTGATATGATGTTACTAACTTTTTGTGAGTTCGATGTGATTCTA
195 TTCAAGGCTGCGAATTTCCTGCTGATATGATGTTACTAACTTTTTGTGAGTTCGATGTGATTCTA
*
22122050 GACATGGCTTGGTTATCTGAGCACGATGCAGAAGTAAACTGCAAGCAGAGACAAATTGATTTAAA
260 GACATGGCTTGGTTATCTGAGCACGATGCAGAAGTAAACTGCAAGAAGAGACAAATTGATTTAAA
22122115 ATG
325 ATG
22122118 CCCAACTCGT
Statistics
Matches: 311, Mismatches: 15, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
327 2 0.01
328 309 0.99
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (328 bp):
TGGTATATTCTATCTCTATGATGTAATTGTGTATGCTTTGATTGACTCAAGGTCAACTCATTCTT
ATATCTATACTACTTTAGCAACTGACAAAAATTTATCTGTCGAGTCAACTGAATTTAATATGCTA
GTCACAAACCCGTTGGGTCATAGTGTTATAATAATTTTGATGTGCCATAAATGTTCACTAAAAGT
TCAAGGCTGCGAATTTCCTGCTGATATGATGTTACTAACTTTTTGTGAGTTCGATGTGATTCTAG
ACATGGCTTGGTTATCTGAGCACGATGCAGAAGTAAACTGCAAGAAGAGACAAATTGATTTAAAA
TGT
Found at i:22123892 original size:609 final size:610
Alignment explanation
Indices: 22121791--22124078 Score: 3519
Period size: 611 Copynumber: 3.8 Consensus size: 610
22121781 TTTAAAATGT
* * * * *
22121791 TGGTATATTCTATCTCTATGATGTAATTGTGTATGCTTTGATTGACTCTGGTTCAACTCATTCTT
1 TGGTATATTCTATCTTTTTGATGTAATTGTGTGTGCTTTGATTGACTCAGGGTCAACTCATTCTT
* * *
22121856 ATATCTATACTACTTTAGCAACTGACAAAAATTTGTCTGTCGAGTCAACTGAATTTAATATGCTA
66 ATATCTATACTACTTTAGCAACTGATAAAAATTTGTCTGTCGAGTCAACTGAATTTGATATGCAA
*
22121921 GTCACAAACCCGTTGGGTCATAGTGTTATAATAATTTTGATGTGCCATAAATGTTCACTAAAAGT
131 GTCACAAACCCGTTGGGTCATAGTGTTATAATAATTTTGATGTGCCATAAATGTCCACTAAAAGT
* * * *
22121986 TCAAGGCTGCGAATTTCCTGCTGATATGATGTTACTAACTTTTTGTGAGTTCGATGTGATTCTAG
196 TCAAGGCTGTGAATTTCCTGCTGATATGATGTTACTACCTTTTTATGAGTTCGATGTGATTCTGG
** *
22122051 ACATGGCTTGGTTATCTGAGCACGATGCAGA-AGTAAACTGCAAGCAGAGACAAATTGATTTAAA
261 GTATGGCTTGGTTATCTGAGCACGATGC-GATAGTAAACTGCAAGCAGAGACAGATTGATTTAAA
* *
22122115 ATGCCCAACTCGTGAGATAATTACAGTTGAATCTGGTAAATTGAATAGTGAGGTTAAAGTGATTT
325 ATGCCCAACTGGTGAGATAATTACAGTTGAATCTGGTAAATTGAACAGTGAGGTTAAAGTGATTT
* * * * *
22122180 AAGCTATTACTGCACAGAAACTGGTCTGTAAGGGCTGCGAGGCATTTCTAGCTTACATACTGGGT
390 CAGCTATTACTACACAAAAACTGGTCCGTAAGGGCTGCGAGGCATTTCTAGCTTACATACTGGAT
* *
22122245 ACTCACTGC-AAAAGGTTAGACGACCAGGTCAAAGCAGTAATATGCGCAA-AAATTGTAATGGTA
455 ACTCACTGCAAAAAGG-TAGACGACCAGGTCAGAGCAGTAATATG-GGAAGAAATTGTAATGGTA
* * *
22122308 CTAATGATAATGCAAACAGGTCTGAGGTTCGAGCACCTACACGGACATATGTCATTCGAGCCAAA
518 ATAATGATAATGCAAACAGGTTTGAGGTTCGAGCGCCTACACGGACA-ATGTCATTCGAGCCAAA
*
22122373 GAAGAGGCTACTGCACCTGATGTTATGAT
582 GAAGAGGCTACTGCACCTGATGTTATGAC
* * *
22122402 TGGTATATTATATCTTTTTGATGTAATTGTGTGTTG-TTTGATTGACTTAGGGTCGACTCATTCT
1 TGGTATATTCTATCTTTTTGATGTAATTGTGTG-TGCTTTGATTGACTCAGGGTCAACTCATTCT
*
22122466 TATATCTATACTACTTTAGCAACTGATAAAAATTTTTCTGTCGAGTCAACTGAATTTGATATGCA
65 TATATCTATACTACTTTAGCAACTGATAAAAATTTGTCTGTCGAGTCAACTGAATTTGATATGCA
* * * * *
22122531 AGTCACAAACCCATTGGGTCATAGTGTTATAGTAATTTTGGTGTGCTATAAATGTCCACTGAAAG
130 AGTCACAAACCCGTTGGGTCATAGTGTTATAATAATTTTGATGTGCCATAAATGTCCACTAAAAG
* *
22122596 TTCAAGGTTGTGAATTTCCTACTGATATGATGTTACTACCTTTTTATGAGTTCGATGTGATTCTG
195 TTCAAGGCTGTGAATTTCCTGCTGATATGATGTTACTACCTTTTTATGAGTTCGATGTGATTCTG
* * * * **
22122661 GGTATGGCTTTGTTATCTGAGCACGAAGCCATAGTAAACTACAAGTTGAGACAGATTGATTTAAA
260 GGTATGGCTTGGTTATCTGAGCACGATGCGATAGTAAACTGCAAGCAGAGACAGATTGATTTAAA
*
22122726 ATGCCCAACTGGTGAGATAATTACAGTTGAATCTGGTAAATTGAACAATGAGGTTAAAGTGATTT
325 ATGCCCAACTGGTGAGATAATTACAGTTGAATCTGGTAAATTGAACAGTGAGGTTAAAGTGATTT
*
22122791 CAGCTATTACTGA-ACAAAAACTGGTCCGTAAGGGCTACGAGGCATTTCTAGCTTACATACTGGA
390 CAGCTATTACT-ACACAAAAACTGGTCCGTAAGGGCTGCGAGGCATTTCTAGCTTACATACTGGA
* * *
22122855 TACTCACTGCAAAAGGGTAGACGACCAGGTTAGAGCAGTAATATGGGCAGAAATTGTAATGGTAA
454 TACTCACTGCAAAAAGGTAGACGACCAGGTCAGAGCAGTAATATGGGAAGAAATTGTAATGGTAA
* * *
22122920 TAATGATAATCCAAACAAGTTTGAGGTTCAAGCGCCTACACGGACATATGTCATTCGAGCCAAAG
519 TAATGATAATGCAAACAGGTTTGAGGTTCGAGCGCCTACACGGACA-ATGTCATTCGAGCCAAAG
22122985 AAGAGGCTACTGCACCTGATGTTATGAC
583 AAGAGGCTACTGCACCTGATGTTATGAC
* * * * *
22123013 TGGTATATTCTATCTTTTTGATGTAATTATGTGTGCTTTGATTAACTCAAGGTCGACTCATTTTT
1 TGGTATATTCTATCTTTTTGATGTAATTGTGTGTGCTTTGATTGACTCAGGGTCAACTCATTCTT
* *
22123078 ATATCTATACTACTTTAGCAACTGATAAAATTTTTTCTGTCGAGTCAACTGAATTTGATATGCAA
66 ATATCTATACTACTTTAGCAACTGATAAAAATTTGTCTGTCGAGTCAACTGAATTTGATATGCAA
* *
22123143 GTCACAAACCTGTTGGGTCATAGTGTTATAATAATTTTGATGTGTCATAAATGTCCACTAAAAGT
131 GTCACAAACCCGTTGGGTCATAGTGTTATAATAATTTTGATGTGCCATAAATGTCCACTAAAAGT
* * * * *
22123208 TCAGGGATGTGAATTTCCTGCTGATATGATGTTATTACCTTTTTGTGAGTTTGATGTGATTCTGG
196 TCAAGGCTGTGAATTTCCTGCTGATATGATGTTACTACCTTTTTATGAGTTCGATGTGATTCTGG
* * *
22123273 GTATGGCTTGGTTATCTGAGCACGATGCGGTGGTAAACTGCAAGTAGAGACAGATTGATTTAAAA
261 GTATGGCTTGGTTATCTGAGCACGATGCGATAGTAAACTGCAAGCAGAGACAGATTGATTTAAAA
* * *
22123338 TGCCCGACTGATGAGATAGTTACAGTTGAATCTGGTAAATTGAACAGTGAGGTTAAAGTGATTTC
326 TGCCCAACTGGTGAGATAATTACAGTTGAATCTGGTAAATTGAACAGTGAGGTTAAAGTGATTTC
* * * * * *
22123403 AGCTATTACTACACAGAAATTAGTCCGTAAGGGCTGTGAGCCATTTCTAGCTTACATACTAGATA
391 AGCTATTACTACACAAAAACTGGTCCGTAAGGGCTGCGAGGCATTTCTAGCTTACATACTGGATA
*
22123468 CTCACTGCAAAAAGGTAGATGACCAGGTCAGAGCAGTAATATGGGAAGAAATTGTAATGGTAATA
456 CTCACTGCAAAAAGGTAGACGACCAGGTCAGAGCAGTAATATGGGAAGAAATTGTAATGGTAATA
*
22123533 ATGATAATGCAAACAGGTTTGAGGTTCGAGCGCCTGCACGGAC-ATGTCATTCGAGCCAAAGAAG
521 ATGATAATGCAAACAGGTTTGAGGTTCGAGCGCCTACACGGACAATGTCATTCGAGCCAAAGAAG
*
22123597 AGGCTACTGCACCTGATGTTTTGAC
586 AGGCTACTGCACCTGATGTTATGAC
*
22123622 TGGTATATTCTATCTTTTTGATGTAATTGTATGTGCTTTGATTGACTCAGGGTCAACTCATTCTT
1 TGGTATATTCTATCTTTTTGATGTAATTGTGTGTGCTTTGATTGACTCAGGGTCAACTCATTCTT
* * * *
22123687 ATATCTATACTACTTTAGCAACTAATAAAAAATTGTCTATCAAGTCAACTGAATTTGATATGCAA
66 ATATCTATACTACTTTAGCAACTGATAAAAATTTGTCTGTCGAGTCAACTGAATTTGATATGCAA
* * *
22123752 GTCACAAACCCGTTGGGTCATAGTGTTATAGTAATTTTGATGTGCCATAAATGTCTACTGAAAGT
131 GTCACAAACCCGTTGGGTCATAGTGTTATAATAATTTTGATGTGCCATAAATGTCCACTAAAAGT
* * * *
22123817 TCAAGGCTATGAATTCCCTGTTGATATGATGTTGCTACCTTTTTATGAGTTCGATGTGATTCTGG
196 TCAAGGCTGTGAATTTCCTGCTGATATGATGTTACTACCTTTTTATGAGTTCGATGTGATTCTGG
* *
22123882 GTATGGCTTGGTTATTTGAGCACGATGCGATGGTAAACTGCAAGCAGAGACAGATTGATTTAAAA
261 GTATGGCTTGGTTATCTGAGCACGATGCGATAGTAAACTGCAAGCAGAGACAGATTGATTTAAAA
* * * * *
22123947 TGCCCGACTGGTGAGATAATTACAGTTGAATCTAGTAAATTGAATAGAGAGGTTAAAGTGATTTT
326 TGCCCAACTGGTGAGATAATTACAGTTGAATCTGGTAAATTGAACAGTGAGGTTAAAGTGATTTC
* * *
22124012 AGCTATTACTGCA-AAAAACTGGTCCGTAAGGGCTGCGTGGCATTTCTAGCTTACATACTTGATA
391 AGCTATTACTACACAAAAACTGGTCCGTAAGGGCTGCGAGGCATTTCTAGCTTACATACTGGATA
22124076 CTC
456 CTC
22124079 GAGGATCAGA
Statistics
Matches: 1526, Mismatches: 144, Indels: 17
0.90 0.09 0.01
Matches are distributed among these distances:
608 47 0.03
609 412 0.27
610 6 0.00
611 1054 0.69
612 7 0.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (610 bp):
TGGTATATTCTATCTTTTTGATGTAATTGTGTGTGCTTTGATTGACTCAGGGTCAACTCATTCTT
ATATCTATACTACTTTAGCAACTGATAAAAATTTGTCTGTCGAGTCAACTGAATTTGATATGCAA
GTCACAAACCCGTTGGGTCATAGTGTTATAATAATTTTGATGTGCCATAAATGTCCACTAAAAGT
TCAAGGCTGTGAATTTCCTGCTGATATGATGTTACTACCTTTTTATGAGTTCGATGTGATTCTGG
GTATGGCTTGGTTATCTGAGCACGATGCGATAGTAAACTGCAAGCAGAGACAGATTGATTTAAAA
TGCCCAACTGGTGAGATAATTACAGTTGAATCTGGTAAATTGAACAGTGAGGTTAAAGTGATTTC
AGCTATTACTACACAAAAACTGGTCCGTAAGGGCTGCGAGGCATTTCTAGCTTACATACTGGATA
CTCACTGCAAAAAGGTAGACGACCAGGTCAGAGCAGTAATATGGGAAGAAATTGTAATGGTAATA
ATGATAATGCAAACAGGTTTGAGGTTCGAGCGCCTACACGGACAATGTCATTCGAGCCAAAGAAG
AGGCTACTGCACCTGATGTTATGAC
Found at i:22130980 original size:29 final size:29
Alignment explanation
Indices: 22130947--22131002 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
22130937 TTATTGTGAG
*
22130947 AGACCAACAAGATTTAAGGAAGACTATTT
1 AGACCAACAAGAATTAAGGAAGACTATTT
*
22130976 AGACCAACCAGAATTAAGGAAGACTAT
1 AGACCAACAAGAATTAAGGAAGACTAT
22131003 CTTTCAGCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.20
Consensus pattern (29 bp):
AGACCAACAAGAATTAAGGAAGACTATTT
Found at i:22132626 original size:23 final size:25
Alignment explanation
Indices: 22132588--22132643 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 25
22132578 AATTATAGTT
*
22132588 TTCTCTTTTATCTTCTCT-C-TTTC
1 TTCTCTTTCATCTTCTCTCCTTTTC
* *
22132611 TTCTCTTTCATTTTCTTTCCTTTTC
1 TTCTCTTTCATCTTCTCTCCTTTTC
22132636 TTCT-TTTC
1 TTCTCTTTC
22132644 TTCACGAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.54
24 5 0.18
25 8 0.29
ACGTcount: A:0.04, C:0.29, G:0.00, T:0.68
Consensus pattern (25 bp):
TTCTCTTTCATCTTCTCTCCTTTTC
Found at i:22134198 original size:23 final size:22
Alignment explanation
Indices: 22134134--22134194 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 22
22134124 GTTCATGAAC
22134134 AAGCTCGTTTA-TGTTCATTTA
1 AAGCTCGTTTATTGTTCATTTA
* ***
22134155 AAGCTCCTTTAATAAATCATTTA
1 AAGCTCGTTT-ATTGTTCATTTA
22134178 AAGCTCGTTTATTGTTC
1 AAGCTCGTTTATTGTTC
22134195 CATTACTATA
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
21 9 0.30
22 5 0.17
23 16 0.53
ACGTcount: A:0.28, C:0.16, G:0.11, T:0.44
Consensus pattern (22 bp):
AAGCTCGTTTATTGTTCATTTA
Found at i:22136654 original size:17 final size:17
Alignment explanation
Indices: 22136634--22136666 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
22136624 TATGGGCATG
*
22136634 AGTCCAGGATGGGTATA
1 AGTCCAGCATGGGTATA
22136651 AGTCCAGCATGGGTAT
1 AGTCCAGCATGGGTAT
22136667 GTAAATCTTT
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:0.27, C:0.15, G:0.33, T:0.24
Consensus pattern (17 bp):
AGTCCAGCATGGGTATA
Found at i:22138305 original size:19 final size:19
Alignment explanation
Indices: 22138283--22138327 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
22138273 ATTTAATTTT
22138283 TTTAAATTGAAATAAT-ATA
1 TTTAAATT-AAATAATGATA
*
22138302 TTTAAATTAATTAATGATA
1 TTTAAATTAAATAATGATA
22138321 TTATAAA
1 TT-TAAA
22138328 AATTAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 6 0.26
19 13 0.57
20 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (19 bp):
TTTAAATTAAATAATGATA
Found at i:22140886 original size:15 final size:15
Alignment explanation
Indices: 22140866--22140905 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
22140856 ACCATTAAGC
22140866 CCAAACCAAGGTGAA
1 CCAAACCAAGGTGAA
**
22140881 CCAAACCAATTTGAA
1 CCAAACCAAGGTGAA
22140896 CCAAGACCAA
1 CCAA-ACCAA
22140906 ACCCAAACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.47, C:0.30, G:0.12, T:0.10
Consensus pattern (15 bp):
CCAAACCAAGGTGAA
Found at i:22140968 original size:7 final size:7
Alignment explanation
Indices: 22140956--22141023 Score: 68
Period size: 7 Copynumber: 10.0 Consensus size: 7
22140946 GTTGATCGAA
22140956 CGTTGAC
1 CGTTGAC
22140963 CGTTGAC
1 CGTTGAC
*
22140970 CGTTGGC
1 CGTTGAC
22140977 CGTTGA-
1 CGTTGAC
*
22140983 CTTTGAC
1 CGTTGAC
22140990 CGTTGAC
1 CGTTGAC
**
22140997 TATTGA-
1 CGTTGAC
*
22141003 CTTTGAC
1 CGTTGAC
*
22141010 CGTTGAT
1 CGTTGAC
22141017 CGTTGAC
1 CGTTGAC
22141024 TTTTTCGGAA
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
6 9 0.19
7 39 0.81
ACGTcount: A:0.15, C:0.24, G:0.26, T:0.35
Consensus pattern (7 bp):
CGTTGAC
Found at i:22140990 original size:20 final size:20
Alignment explanation
Indices: 22140965--22141026 Score: 88
Period size: 20 Copynumber: 3.1 Consensus size: 20
22140955 ACGTTGACCG
*
22140965 TTGACCGTTGGCCGTTGACT
1 TTGACCGTTGACCGTTGACT
**
22140985 TTGACCGTTGACTATTGACT
1 TTGACCGTTGACCGTTGACT
*
22141005 TTGACCGTTGATCGTTGACT
1 TTGACCGTTGACCGTTGACT
22141025 TT
1 TT
22141027 TTCGGAAAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.15, C:0.21, G:0.24, T:0.40
Consensus pattern (20 bp):
TTGACCGTTGACCGTTGACT
Found at i:22156637 original size:16 final size:18
Alignment explanation
Indices: 22156606--22156643 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
22156596 TTTCCTTCTT
22156606 TTATATTTATTAATATTA
1 TTATATTTATTAATATTA
22156624 TTATA-TTA-TAATATTA
1 TTATATTTATTAATATTA
22156640 TTAT
1 TTAT
22156644 TAATTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 12 0.60
17 3 0.15
18 5 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTATATTTATTAATATTA
Found at i:22162771 original size:18 final size:18
Alignment explanation
Indices: 22162748--22162786 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
22162738 AAAAATCAAA
*
22162748 TTTCACTTCAATTCT-ATT
1 TTTCACATC-ATTCTCATT
22162766 TTTCACATCATTCTCATT
1 TTTCACATCATTCTCATT
22162784 TTT
1 TTT
22162787 GTCCCATATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.21, C:0.23, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTCACATCATTCTCATT
Found at i:22163815 original size:16 final size:18
Alignment explanation
Indices: 22163780--22163817 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
22163770 TTTCCTTCTT
*
22163780 TTATATTTATTAATATTA
1 TTATATTTATTAATAATA
22163798 TTATA-TTA-TAATAATA
1 TTATATTTATTAATAATA
22163814 TTAT
1 TTAT
22163818 TAATTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 11 0.58
17 3 0.16
18 5 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTATATTTATTAATAATA
Found at i:22164916 original size:83 final size:82
Alignment explanation
Indices: 22164687--22164930 Score: 221
Period size: 83 Copynumber: 3.0 Consensus size: 82
22164677 AATTACTTCT
* ** * *
22164687 TTGTTTGGAAACAAAATTAAAATCAAATCAAATTTGTTGAACGGCGGGAATAAATACCAAAACAA
1 TTGTTTGGAAACAAAA-TAAAAT-AAATAAAATTTGTTGAACGATGGGAATAAATACCGAAACAG
* * * *
22164752 AATTGTTTAATTTTAATTC
64 ATTTATTCAATCTTAATTC
* * ** *
22164771 TTGTTTGGAAACCAAAT--AA-AAATAAAATATGTTGAAC-AGTGGGAATAAATATTGAAAAAGA
1 TTGTTTGGAAACAAAATAAAATAAATAAAATTTGTTGAACGA-TGGGAATAAATACCGAAACAGA
22164832 TTTATTCAA-CTT-ATTC
65 TTTATTCAATCTTAATTC
* * *
22164848 TTGTTTTGGAAACAAAATCAAAATGAAATGAAATTTGTTAAACGATGGGAATAAATCCCGAAACA
1 TTG-TTTGGAAACAAAAT-AAAAT-AAATAAAATTTGTTGAACGATGGGAATAAATACCGAAACA
* *
22164913 GATTTATTCGATTTTAAT
63 GATTTATTCAATCTTAAT
22164931 ATTTTATTCA
Statistics
Matches: 126, Mismatches: 24, Indels: 19
0.75 0.14 0.11
Matches are distributed among these distances:
77 7 0.06
78 15 0.12
79 38 0.30
81 4 0.03
83 42 0.33
84 18 0.14
85 2 0.02
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.32
Consensus pattern (82 bp):
TTGTTTGGAAACAAAATAAAATAAATAAAATTTGTTGAACGATGGGAATAAATACCGAAACAGAT
TTATTCAATCTTAATTC
Found at i:22167164 original size:3 final size:3
Alignment explanation
Indices: 22167156--22167190 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
22167146 TCATGTATAA
*
22167156 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAA CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA
22167191 ACAACAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.37, C:0.34, G:0.29, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:22171095 original size:108 final size:108
Alignment explanation
Indices: 22170942--22171374 Score: 661
Period size: 108 Copynumber: 4.0 Consensus size: 108
22170932 GGAACTTTAT
* * * *
22170942 AACAACATTGATGCAAAACTTAATTCAATGTAATTAAGGAGGATGGTTCAAACTAACACGAATGA
1 AACAACATTGATGCAAAACTTAATTCAATATAATTAAGGATGATGGTTCAAACTAACATGAACGA
*
22171007 AAGATTCAAAAGTTATTTGC-CGAGCTTGCTCTAGCATTTGGCA
66 AAGCTTCAAAAGTTATTTGCTC-AGCTTGCTCTAGCATTTGGCA
* * * *
22171050 AGCAACATTGATGCAAAACTTACTACAATATAATTAAGGATGATGGTTCAAACTAATATGAACGA
1 AACAACATTGATGCAAAACTTAATTCAATATAATTAAGGATGATGGTTCAAACTAACATGAACGA
**
22171115 AAGCTTCAAAAGTTATTTGCTCAGCTTGCTCTAGCATTTAACA
66 AAGCTTCAAAAGTTATTTGCTCAGCTTGCTCTAGCATTTGGCA
* * *
22171158 AACAACATTGATGCAAAACTTAATTCAATATAATTAAGGATGATGGTTCAAACTAATAAGAAAGA
1 AACAACATTGATGCAAAACTTAATTCAATATAATTAAGGATGATGGTTCAAACTAACATGAACGA
* * * *
22171223 TAGCTTCAAGACTTATTTGCTCAGCTTGCTCTAGCATTTGGAA
66 AAGCTTCAAAAGTTATTTGCTCAGCTTGCTCTAGCATTTGGCA
* *
22171266 AACAACATTGATGCAAAACTTAATTCAATATAATTATGGATGATGGTTCAAACTAACATGAACCA
1 AACAACATTGATGCAAAACTTAATTCAATATAATTAAGGATGATGGTTCAAACTAACATGAACGA
*
22171331 ATGCTTCAAAAGTTATTTGCTCAGCTTGCTCTAGCATTTGGCA
66 AAGCTTCAAAAGTTATTTGCTCAGCTTGCTCTAGCATTTGGCA
22171374 A
1 A
22171375 TTTCTATTTT
Statistics
Matches: 292, Mismatches: 32, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
108 291 1.00
109 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (108 bp):
AACAACATTGATGCAAAACTTAATTCAATATAATTAAGGATGATGGTTCAAACTAACATGAACGA
AAGCTTCAAAAGTTATTTGCTCAGCTTGCTCTAGCATTTGGCA
Found at i:22174235 original size:11 final size:11
Alignment explanation
Indices: 22174221--22174303 Score: 60
Period size: 11 Copynumber: 7.5 Consensus size: 11
22174211 CACCACTTCT
22174221 CCACCATAGCA
1 CCACCATAGCA
* *
22174232 CCACCGTACCA
1 CCACCATAGCA
*
22174243 CCACCCA-AGTA
1 CCA-CCATAGCA
* *
22174254 TCACCATACCA
1 CCACCATAGCA
*
22174265 CCAGCATAGCA
1 CCACCATAGCA
* *
22174276 TCACCATATCA
1 CCACCATAGCA
* *
22174287 CCACCCTTGCA
1 CCACCATAGCA
22174298 CCACCA
1 CCACCA
22174304 CAAAACTATT
Statistics
Matches: 51, Mismatches: 19, Indels: 4
0.69 0.26 0.05
Matches are distributed among these distances:
10 3 0.06
11 46 0.90
12 2 0.04
ACGTcount: A:0.33, C:0.47, G:0.07, T:0.13
Consensus pattern (11 bp):
CCACCATAGCA
Done.