Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001840.1 Hibiscus syriacus cultivar Beakdansim tig00003725_pilon, whole genome shotgun sequence
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: 2412736
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 12
Found at i:1042565 original size:18 final size:18
Alignment explanation
Indices: 1042542--1042581 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
1042532 CCAGCAGCCA
1042542 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
1042560 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
1042578 CCGC
1 CCGC
1042582 CATTGCCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.25, C:0.33, G:0.23, T:0.20
Consensus pattern (18 bp):
CCGCAGCCATATATGATG
Found at i:1044178 original size:190 final size:188
Alignment explanation
Indices: 1043854--1044231 Score: 706
Period size: 190 Copynumber: 2.0 Consensus size: 188
1043844 AAGGACCGTT
1043854 GTATACTGTTAGTTCTCATCTTTTGTTTTTTCTCTTCCTCTTCGATACGCGAACCATCCAATTGC
1 GTATACTGTTAGTTCTCATCTTTTGTTTTTTCTCTTCCTCTTCGATACGCGAACCATCCAATTGC
1043919 ATCCGTTTTCGCGCTGGGCACAGTAGCATACATATTTTTCGATCGTGGAGCGGTCTACTCTGGAC
66 ATCCGTTTTCGCGCTGGGCACAGTAGCATACATATTTTTCGATCGTGGAGCGGTCTACTCTGGAC
1043984 TGAACAGAATTACG-ATATTGTAATTTTTGATAGCCATCACCGCTTCTTCTTTTCTTGAAAA
131 TGAACAG-ATTACGAATATTGTAA-TTTTGATAGCCATCACCGCTTC-TC-TTTCTTGAAAA
1044045 GTATACTGTTAGTTCTCATCTTTTGTTTTTTCTCTTCCTC-TCGATACGCGAACCATCCAATTGC
1 GTATACTGTTAGTTCTCATCTTTTGTTTTTTCTCTTCCTCTTCGATACGCGAACCATCCAATTGC
1044109 ATCCGTTTTCGCGCTGGGCACAGTAGCATACATATTTTTCGATCGTGGAGCGGTCTACTCTGGAC
66 ATCCGTTTTCGCGCTGGGCACAGTAGCATACATATTTTTCGATCGTGGAGCGGTCTACTCTGGAC
1044174 TGAACAGATTACGAATATTGTAATTTTGATAGCCATCACCGCTTCTCTTTCTTGAAAA
131 TGAACAGATTACGAATATTGTAATTTTGATAGCCATCACCGCTTCTCTTTCTTGAAAA
1044232 CTCCATGCCT
Statistics
Matches: 186, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
187 11 0.06
188 2 0.01
189 28 0.15
190 105 0.56
191 40 0.22
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.38
Consensus pattern (188 bp):
GTATACTGTTAGTTCTCATCTTTTGTTTTTTCTCTTCCTCTTCGATACGCGAACCATCCAATTGC
ATCCGTTTTCGCGCTGGGCACAGTAGCATACATATTTTTCGATCGTGGAGCGGTCTACTCTGGAC
TGAACAGATTACGAATATTGTAATTTTGATAGCCATCACCGCTTCTCTTTCTTGAAAA
Found at i:1045769 original size:49 final size:51
Alignment explanation
Indices: 1045662--1045784 Score: 189
Period size: 49 Copynumber: 2.5 Consensus size: 51
1045652 TTATACAAAA
1045662 CGCGGTACCTGCCCCGCGCTATATAAAATTATGTGAGGAGTAAATGTATGT
1 CGCGGTACCTGCCCCGCGCTATATAAAATTATGTGAGGAGTAAATGTATGT
*
1045713 GGCGGTACCTGCCCCGCGCTATATAAAATTAT-T-AGGAGTAAATGTATAG-
1 CGCGGTACCTGCCCCGCGCTATATAAAATTATGTGAGGAGTAAATGTAT-GT
**
1045762 CGCGGTACCTGATCCGCGCTATA
1 CGCGGTACCTGCCCCGCGCTATA
1045785 CCCTTACGTG
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
49 34 0.51
50 2 0.03
51 31 0.46
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.26
Consensus pattern (51 bp):
CGCGGTACCTGCCCCGCGCTATATAAAATTATGTGAGGAGTAAATGTATGT
Found at i:1045901 original size:51 final size:51
Alignment explanation
Indices: 1045796--1045912 Score: 139
Period size: 51 Copynumber: 2.3 Consensus size: 51
1045786 CCTTACGTGG
* * * **
1045796 CGTATAGCGCGCTTC-AGGGGCCGCGCTATACCCATGTGGCGCCAGCTCAC
1 CGTATAGCGCGGTGCAAGGGGCCGCGCTATACCCACGTGGCGCCAAATCAC
* *
1045846 CGTATAGCGCGGTGCAAGGGG-CGCGCTATACCCCACGTGGCGCCAAATTAT
1 CGTATAGCGCGGTGCAAGGGGCCGCGCTATA-CCCACGTGGCGCCAAATCAC
*
1045897 CGTATAACGCGGTGCA
1 CGTATAGCGCGGTGCA
1045913 TGCGCGCTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
50 22 0.39
51 35 0.61
ACGTcount: A:0.20, C:0.32, G:0.31, T:0.18
Consensus pattern (51 bp):
CGTATAGCGCGGTGCAAGGGGCCGCGCTATACCCACGTGGCGCCAAATCAC
Found at i:1049436 original size:56 final size:56
Alignment explanation
Indices: 1049350--1049461 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
1049340 GAGGAATGCT
1049350 GACTGGAGTTTCTGCTTAATGAATCTTTAATTTTGAAATTTAAAATTCTTGAACTC
1 GACTGGAGTTTCTGCTTAATGAATCTTTAATTTTGAAATTTAAAATTCTTGAACTC
1049406 GACTGGAGTTTCTGCTTAATGAATCTTTAATTTTGAAATTTAAAATTCTTGAACTC
1 GACTGGAGTTTCTGCTTAATGAATCTTTAATTTTGAAATTTAAAATTCTTGAACTC
1049462 CTATCGCTGG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.43
Consensus pattern (56 bp):
GACTGGAGTTTCTGCTTAATGAATCTTTAATTTTGAAATTTAAAATTCTTGAACTC
Found at i:1055175 original size:26 final size:26
Alignment explanation
Indices: 1055146--1055200 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
1055136 AGTACTTGAT
1055146 TACACAGAGAACTTACATAAAAAATC
1 TACACAGAGAACTTACATAAAAAATC
* *
1055172 TACACAGAGAACTTACATGAAAGATC
1 TACACAGAGAACTTACATAAAAAATC
1055198 TAC
1 TAC
1055201 TCAAATTAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.49, C:0.20, G:0.11, T:0.20
Consensus pattern (26 bp):
TACACAGAGAACTTACATAAAAAATC
Found at i:1055555 original size:55 final size:54
Alignment explanation
Indices: 1055471--1055579 Score: 191
Period size: 55 Copynumber: 2.0 Consensus size: 54
1055461 AATTGAATTC
1055471 AAGTCTTTTCAAGTTTAGATGTACGAGACTACTTAGTCTTCACATTGTTAAGAT
1 AAGTCTTTTCAAGTTTAGATGTACGAGACTACTTAGTCTTCACATTGTTAAGAT
* *
1055525 AAGTCTTGTTCAAGTTTAGATGTACTAGACTACTTAGTCTTCATATTGTTAAGAT
1 AAGTCTT-TTCAAGTTTAGATGTACGAGACTACTTAGTCTTCACATTGTTAAGAT
1055580 CATCACAAGT
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
54 7 0.13
55 45 0.87
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (54 bp):
AAGTCTTTTCAAGTTTAGATGTACGAGACTACTTAGTCTTCACATTGTTAAGAT
Found at i:1074258 original size:91 final size:90
Alignment explanation
Indices: 1074163--1074434 Score: 449
Period size: 90 Copynumber: 3.0 Consensus size: 90
1074153 AATTTTAGTG
*
1074163 ATCCAAATTTTTGATTATCTAAAATTTTAGATCAGATAATGTACGATATCCAATAATACACACCT
1 ATCCAAATTTTTGAATATCTAAAATTTTAGATC-GATAATGTACGATATCCAATAATACACACCT
1074228 CTATTGTTATCTATCAAATATTTTTT
65 CTATTGTTATCTATCAAATATTTTTT
1074254 ATCCAAATTTTTGAATATCTAAAATTTTAGATCGGATAATGTACG-TATCCAATAATACACACCT
1 ATCCAAATTTTTGAATATCTAAAATTTTAGATC-GATAATGTACGATATCCAATAATACACACCT
*
1074318 CTATTGTTATCTATCAAATA-ATTTT
65 CTATTGTTATCTATCAAATATTTTTT
* * *
1074343 ATCCAAATTTTTGAATATCTAAAATTTTAGATCGAATAATTTACAATATCCAATAATACACACCC
1 ATCCAAATTTTTGAATATCTAAAATTTTAGATCG-ATAATGTACGATATCCAATAATACACACCT
1074408 CTATTGTTATCTATCAAATAATTTTTT
65 CTATTGTTATCTATCAAAT-ATTTTTT
1074435 CCCAACAGCA
Statistics
Matches: 170, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
88 1 0.01
89 45 0.26
90 76 0.45
91 44 0.26
92 4 0.02
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.40
Consensus pattern (90 bp):
ATCCAAATTTTTGAATATCTAAAATTTTAGATCGATAATGTACGATATCCAATAATACACACCTC
TATTGTTATCTATCAAATATTTTTT
Found at i:1075545 original size:58 final size:60
Alignment explanation
Indices: 1075435--1075549 Score: 162
Period size: 58 Copynumber: 1.9 Consensus size: 60
1075425 AAATAGTTGG
* * **
1075435 ATGACCATTTTATAATTTTTAATAGTCTAAGGACTCAACAAAATAATATCTTATAATTAA
1 ATGACCATTTTATAACTTTTAATAATCTAACAACTCAACAAAATAATATCTTATAATTAA
* *
1075495 ATGACTATTTTATAACTTTTAA-AAT-TAACAACTCAATAAAATAATATCTTATAAT
1 ATGACCATTTTATAACTTTTAATAATCTAACAACTCAACAAAATAATATCTTATAAT
1075550 AATGAATCAT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
58 27 0.55
59 2 0.04
60 20 0.41
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.39
Consensus pattern (60 bp):
ATGACCATTTTATAACTTTTAATAATCTAACAACTCAACAAAATAATATCTTATAATTAA
Found at i:1080391 original size:10 final size:10
Alignment explanation
Indices: 1080376--1080400 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1080366 CATCCTCTGC
1080376 AAGAAAAAAA
1 AAGAAAAAAA
1080386 AAGAAAAAAA
1 AAGAAAAAAA
1080396 AAGAA
1 AAGAA
1080401 CCCGTGAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:1081779 original size:148 final size:145
Alignment explanation
Indices: 1081479--1081752 Score: 319
Period size: 148 Copynumber: 1.9 Consensus size: 145
1081469 AATAATTTCA
* *
1081479 TAATATTTATTTAATATTAATATTAAGAAATGGGCTGTCTTAAAGCACCTAGAAGTCCTTTTCTG
1 TAATATTTATTTAATATTAATATTAAGAAATGGGCTGTCTTAAAACACCTAGAAGTCCTTTTCTA
* * * *
1081544 ATATTCTTAAATAAATAAATATCCTATTTTTATAAATTATATATATTAATTTATTTTAATTATAT
66 ATATTCTTAAATAAATAAATA--CTATTTTAATAAATTATATATATTAAATTATATTAATTAAAT
* * *
1081609 TTAGAGAAATGTTTTAT
129 TTAAAGAAAAGTTTAAT
* * *
1081626 TAATATTTATTTATTTTTTAATATTAAGAAATGGGCTGTCTTAAAACACCTAGAAGTCTTTTTCT
1 TAATATTTATTTA-ATATTAATATTAAGAAATGGGCTGTCTTAAAACACCTAGAAGTCCTTTTCT
* *
1081691 AATATT-TCTAAGTAAATAAATA-TATTATTAATATATT-T-T-T-TTAAAATTATATTAA-TAA
65 AATATTCT-TAAATAAATAAATACTATT-TTAATAAATTATATATATT-AAATTATATTAATTAA
1081749 ATTT
127 ATTT
1081753 GAAATAACAA
Statistics
Matches: 112, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
142 8 0.07
143 11 0.10
144 1 0.01
145 5 0.04
146 8 0.07
147 14 0.12
148 65 0.58
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (145 bp):
TAATATTTATTTAATATTAATATTAAGAAATGGGCTGTCTTAAAACACCTAGAAGTCCTTTTCTA
ATATTCTTAAATAAATAAATACTATTTTAATAAATTATATATATTAAATTATATTAATTAAATTT
AAAGAAAAGTTTAAT
Found at i:1089628 original size:75 final size:75
Alignment explanation
Indices: 1089522--1089681 Score: 212
Period size: 75 Copynumber: 2.1 Consensus size: 75
1089512 AAATAAATGA
* * * * **
1089522 GCATGCTGAAAACCCCTTTCAATCAGAATCAGGAATGTTGACGCATTTTGAACATTTGTATCAGC
1 GCATGTTGAAAACCCATTTCAATCAGAATCAGGAATGATGACACATTTTGAACATTCATATCAGC
*
1089587 AAATGTTGGG
66 AAATGTTAGG
* * *
1089597 GCATGTTGAAAGCCCATTTCAATCATAATCAGGAATGATGACACATTTTGAACGTTCATATCAGC
1 GCATGTTGAAAACCCATTTCAATCAGAATCAGGAATGATGACACATTTTGAACATTCATATCAGC
*
1089662 AATTGTTAGG
66 AAATGTTAGG
*
1089672 GCATATTGAA
1 GCATGTTGAA
1089682 GGCCTATATC
Statistics
Matches: 73, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (75 bp):
GCATGTTGAAAACCCATTTCAATCAGAATCAGGAATGATGACACATTTTGAACATTCATATCAGC
AAATGTTAGG
Found at i:1090975 original size:22 final size:22
Alignment explanation
Indices: 1090945--1091002 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
1090935 TACATCTAGA
*
1090945 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAAATTCT
*
1090967 CTCTCCAAAGATGATAAATTCT
1 CTCTTCAAAGATGATAAATTCT
*
1090989 CTTTTCAAAGATGA
1 CTCTTCAAAGATGA
1091003 AAGCTTTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.34
Consensus pattern (22 bp):
CTCTTCAAAGATGATAAATTCT
Found at i:1091918 original size:73 final size:73
Alignment explanation
Indices: 1091668--1092363 Score: 1108
Period size: 73 Copynumber: 9.5 Consensus size: 73
1091658 CTATTTCCCA
* * *
1091668 CATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAAGCCTTCGAGAGCTTTTTGATGTTTTAA
1 CATCTGTAAGACCTACAGTGCATGATGTTTTC-AAAAAGCCTTCGGGAGCTTTTTGA--TTTTAA
1091733 AGCCTCAGGGT
63 AGCCTCAGGGT
*
1091744 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGATTTTTGATATTTAAAG
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGAT-TTTAAAG
1091809 CCTCAGGGT
65 CCTCAGGGT
* * *
1091818 CATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGTCTTCGAGAGCTTTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
1091883 CTCAGGGT
66 CTCAGGGT
*
1091891 CATCTGTAAGACCTACAGTGAATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
1091956 CTCAGGGT
66 CTCAGGGT
* * * * *
1091964 CATCTGTAAGACTTACAGTGCATGATGTTTTCAAAAAGCCTTTGGGAACTTTTTTATATTGAAAG
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGAT-TTTAAAG
1092029 CCTCAGGGT
65 CCTCAGGGT
* *
1092038 CATCTATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGATTTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
*
1092103 CTTAGGGT
66 CTCAGGGT
* *
1092111 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAACCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
1092176 CTCAGGGT
66 CTCAGGGT
1092184 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAG
1 CATCTGTAAGACCTACAGTGCATGATGTTTTC-AAAAAGCCTTCGGGAGCTTTTTGATTTTAAAG
1092249 CCTCAGGGT
65 CCTCAGGGT
*
1092258 CATCTGTAAGACCTACAGTGTATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
1092323 CTCAGGGT
66 CTCAGGGT
* * * *
1092331 CAT-TCATAAGACCT-CTGGGCAGGATGTTTTCAA
1 CATCT-GTAAGACCTACAGTGCATGATGTTTTCAA
1092364 CATTTCCATC
Statistics
Matches: 577, Mismatches: 39, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
72 16 0.03
73 304 0.53
74 205 0.36
75 22 0.04
76 30 0.05
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (73 bp):
CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
CTCAGGGT
Found at i:1091944 original size:147 final size:146
Alignment explanation
Indices: 1091668--1092363 Score: 1108
Period size: 147 Copynumber: 4.7 Consensus size: 146
1091658 CTATTTCCCA
* * *
1091668 CATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAAGCCTTCGAGAGCTTTTTGATGTTTTAA
1 CATCTGTAAGACCTACAGTGCATGATGTTTTC-AAAAAGCCTTCGGGAGCTTTTTGA--TTTTAA
1091733 AGCCTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGATTTTT
63 AGCCTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGATTTTT
1091798 GATATTTAAAGCCTCAGGGT
128 GAT-TTTAAAGCCTCAGGGT
* * *
1091818 CATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGTCTTCGAGAGCTTTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
* *
1091883 CTCAGGGTCATCTGTAAGACCTACAGTGAATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGAT
66 CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGATTTTTGAT
1091948 TTTAAAGCCTCAGGGT
131 TTTAAAGCCTCAGGGT
* * * * *
1091964 CATCTGTAAGACTTACAGTGCATGATGTTTTCAAAAAGCCTTTGGGAACTTTTTTATATTGAAAG
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGAT-TTTAAAG
*
1092029 CCTCAGGGTCATCTATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGATTTTTGA
65 CCTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGATTTTTGA
*
1092094 TTTTAAAGCCTTAGGGT
130 TTTTAAAGCCTCAGGGT
* *
1092111 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAACCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
*
1092176 CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAAGCCTTCGGGAGCTTTTTGA
66 CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTC-AAAAAGCCTTCGGGAGATTTTTGA
1092241 TTTTAAAGCCTCAGGGT
130 TTTTAAAGCCTCAGGGT
*
1092258 CATCTGTAAGACCTACAGTGTATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
* * * *
1092323 CTCAGGGTCAT-TCATAAGACCT-CTGGGCAGGATGTTTTCAA
66 CTCAGGGTCATCT-GTAAGACCTACAGTGCATGATGTTTTCAA
1092364 CATTTCCATC
Statistics
Matches: 510, Mismatches: 33, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
145 2 0.00
146 126 0.25
147 328 0.64
149 23 0.05
150 31 0.06
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (146 bp):
CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGATTTTTGAT
TTTAAAGCCTCAGGGT
Found at i:1092058 original size:220 final size:220
Alignment explanation
Indices: 1091668--1092363 Score: 1112
Period size: 220 Copynumber: 3.2 Consensus size: 220
1091658 CTATTTCCCA
* * *
1091668 CATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAAGCCTTCGAGAGCTTTTTGATGTTTTAA
1 CATCTGTAAGACCTACAGTGCATGATGTTTTC-AAAAAGCCTTCGGGAGCTTTTTGA--TTTTAA
1091733 AGCCTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGA-TTTT
63 AGCCTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGA-ACTTTT
* *
1091797 TGATATTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGTCTTCG
127 TGATATTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCG
*
1091862 AGAGCTTTTTGATTTTAAAGCCTCAGGGT
192 GGAGCTTTTTGATTTTAAAGCCTCAGGGT
*
1091891 CATCTGTAAGACCTACAGTGAATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
* * *
1091956 CTCAGGGTCATCTGTAAGACTTACAGTGCATGATGTTTTCAAAAAGCCTTTGGGAACTTTTTTAT
66 CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAACTTTTTGAT
* *
1092021 ATTGAAAGCCTCAGGGTCATCTATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAG
131 ATTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAG
* *
1092086 ATTTTTGATTTTAAAGCCTTAGGGT
196 CTTTTTGATTTTAAAGCCTCAGGGT
* *
1092111 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAACCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
*
1092176 CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAAGCCTTCGGGAGCTTTTTGA
66 CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTC-AAAAAGCCTTCGGGAACTTTTTGA
*
1092241 T-TTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGTATGATGTTTTCAAAAAGCCTTCGGGA
130 TATTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGA
1092305 GCTTTTTGATTTTAAAGCCTCAGGGT
195 GCTTTTTGATTTTAAAGCCTCAGGGT
* * * *
1092331 CAT-TCATAAGACCT-CTGGGCAGGATGTTTTCAA
1 CATCT-GTAAGACCTACAGTGCATGATGTTTTCAA
1092364 CATTTCCATC
Statistics
Matches: 440, Mismatches: 30, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
219 18 0.04
220 348 0.79
221 22 0.05
222 23 0.05
223 29 0.07
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (220 bp):
CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAACTTTTTGAT
ATTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAG
CTTTTTGATTTTAAAGCCTCAGGGT
Found at i:1092498 original size:3 final size:3
Alignment explanation
Indices: 1092490--1092550 Score: 52
Period size: 3 Copynumber: 20.0 Consensus size: 3
1092480 CAGTTTACTT
** * * *
1092490 TTA TTA TTA TTA AAA TTC TTA TTA TTA TTA ATA TCA -TA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
1092535 TTTA TTA TTA TTA TTA
1 -TTA TTA TTA TTA TTA
1092551 AATAAAATAC
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
2 1 0.02
3 38 0.84
4 6 0.13
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:1092533 original size:18 final size:18
Alignment explanation
Indices: 1092491--1092536 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1092481 AGTTTACTTT
*
1092491 TATTATTATTAAAATTCT
1 TATTATTATTAAAATTCA
*
1092509 TATTATTATTAATA-TCA
1 TATTATTATTAAAATTCA
1092526 TATATATTATT
1 TAT-TATTATT
1092537 TATTATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTATTATTAAAATTCA
Found at i:1095156 original size:18 final size:18
Alignment explanation
Indices: 1095133--1095167 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1095123 GACCGGTCAT
1095133 GACCCGACCCGTTGACCC
1 GACCCGACCCGTTGACCC
1095151 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
1095168 GTTGACAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.49, G:0.23, T:0.11
Consensus pattern (18 bp):
GACCCGACCCGTTGACCC
Found at i:1095167 original size:13 final size:13
Alignment explanation
Indices: 1095132--1095156 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1095122 TGACCGGTCA
1095132 TGACCCGACCCGT
1 TGACCCGACCCGT
1095145 TGACCCGACCCG
1 TGACCCGACCCG
1095157 ACCCGTTGAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.48, G:0.24, T:0.12
Consensus pattern (13 bp):
TGACCCGACCCGT
Found at i:1095265 original size:30 final size:29
Alignment explanation
Indices: 1095175--1095278 Score: 154
Period size: 29 Copynumber: 3.6 Consensus size: 29
1095165 ACCGTTGACA
*
1095175 GGTGCTATTCTGGTAAATAATTAGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
*
1095204 GGTGCTATTCTGGTAAATAATTCAGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
* *
1095233 GGTGATATTCTTGTAAATAATTCGGTTTTT
1 GGTGCTATTCTGGTAAATAATTCGG-TTTT
*
1095263 GGTGCTTTTCTGGTAA
1 GGTGCTATTCTGGTAA
1095279 TTAAGTCGAA
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
29 49 0.74
30 17 0.26
ACGTcount: A:0.22, C:0.09, G:0.23, T:0.46
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCGGTTTT
Found at i:1097527 original size:21 final size:21
Alignment explanation
Indices: 1097496--1097575 Score: 81
Period size: 21 Copynumber: 3.7 Consensus size: 21
1097486 AAAGTACCAT
* *
1097496 AGTACTCAAAGTACTACTACA
1 AGTACACAAAGTACTACTCCA
* *
1097517 AGTACATAAAGTTCT-CTTGCCA
1 AGTACACAAAGTACTAC-T-CCA
1097539 TAGTACACAAAGTACTACTCCA
1 -AGTACACAAAGTACTACTCCA
*
1097561 AATACACAAAGTACT
1 AGTACACAAAGTACT
1097576 TTTACGAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
20 1 0.02
21 27 0.56
22 5 0.10
23 14 0.29
24 1 0.02
ACGTcount: A:0.41, C:0.24, G:0.10, T:0.25
Consensus pattern (21 bp):
AGTACACAAAGTACTACTCCA
Found at i:1100756 original size:16 final size:17
Alignment explanation
Indices: 1100737--1100769 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1100727 CATATCTCTT
1100737 ATCTCTT-GTTCATATG
1 ATCTCTTAGTTCATATG
1100753 ATCTCTTACGTTCATAT
1 ATCTCTTA-GTTCATAT
1100770 TATATATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.21, C:0.21, G:0.09, T:0.48
Consensus pattern (17 bp):
ATCTCTTAGTTCATATG
Found at i:1101110 original size:18 final size:18
Alignment explanation
Indices: 1101087--1101121 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1101077 CCACTATGAA
1101087 ATGTCCCGAAGGACCACT
1 ATGTCCCGAAGGACCACT
*
1101105 ATGTCCCGAATGACCAC
1 ATGTCCCGAAGGACCAC
1101122 GTAGAACCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.34, G:0.20, T:0.17
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACT
Found at i:1101312 original size:22 final size:25
Alignment explanation
Indices: 1101286--1101334 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
1101276 ATTTTCTCAT
1101286 ATTCAT-ATCA-ATATATCAT-TTC
1 ATTCATAATCACATATATCATGTTC
*
1101308 ATTCATAATCACATATCTCATGTTC
1 ATTCATAATCACATATATCATGTTC
1101333 AT
1 AT
1101335 ATTCTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 6 0.26
23 4 0.17
24 8 0.35
25 5 0.22
ACGTcount: A:0.35, C:0.20, G:0.02, T:0.43
Consensus pattern (25 bp):
ATTCATAATCACATATATCATGTTC
Found at i:1110675 original size:24 final size:24
Alignment explanation
Indices: 1110648--1110723 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
1110638 TATATCAAAA
*
1110648 ATCAAAACATAAAT-CTGGTCAAGT
1 ATCAAAACA-AAATCCAGGTCAAGT
* *
1110672 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
1110696 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
1110720 ATCA
1 ATCA
1110724 GATCAGAATC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 4 0.09
24 41 0.91
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.24
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:1110724 original size:24 final size:24
Alignment explanation
Indices: 1110665--1110780 Score: 171
Period size: 24 Copynumber: 4.8 Consensus size: 24
1110655 CATAAATCTG
* * *
1110665 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
*
1110689 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
*
1110713 GTCAAGTATCAGATCAGAATCTAT
1 GTCAAGTATCAGATCAGAATCCAT
1110737 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
1110761 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
1110781 TCAAATCGAA
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
23 2 0.02
24 80 0.95
25 2 0.02
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:1110810 original size:48 final size:48
Alignment explanation
Indices: 1110696--1110797 Score: 127
Period size: 48 Copynumber: 2.1 Consensus size: 48
1110686 CAGGTCAAGT
* * ** *
1110696 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCTATGTCAGAT
1 ATCAGATCAAAATCCATGTCAAGTATCAGATCAGAATCTAAATCAGAA
*
1110744 ATCAGATCAGAATCCATGTCAAGTATCAGATCAGAAT-TCAAATC-GAA
1 ATCAGATCAAAATCCATGTCAAGTATCAGATCAGAATCT-AAATCAGAA
1110791 ATCAGAT
1 ATCAGAT
1110798 TAAATATTCA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
47 10 0.20
48 39 0.80
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.25
Consensus pattern (48 bp):
ATCAGATCAAAATCCATGTCAAGTATCAGATCAGAATCTAAATCAGAA
Found at i:1115901 original size:24 final size:23
Alignment explanation
Indices: 1115790--1115897 Score: 130
Period size: 24 Copynumber: 4.7 Consensus size: 23
1115780 ATAAATCTGT
* *
1115790 TCAAGTATCATATCAAAATCCAGG
1 TCAAGTATCAGATC-AAATCCATG
*
1115814 TCAAGTATCAGATCAAATCCAAG
1 TCAAGTATCAGATCAAATCCATG
*
1115837 TCAAGTATCAGATC-AATCTATG
1 TCAAGTATCAGATCAAATCCATG
*
1115859 GC-AGATATCAGATCAGAATCCATG
1 TCAAG-TATCAGATCA-AATCCATG
1115883 TCAAGTATCAGATCA
1 TCAAGTATCAGATCA
1115898 GAATTCAATC
Statistics
Matches: 73, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
21 2 0.03
22 16 0.22
23 22 0.30
24 31 0.42
25 2 0.03
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (23 bp):
TCAAGTATCAGATCAAATCCATG
Found at i:1116361 original size:222 final size:222
Alignment explanation
Indices: 1115975--1116419 Score: 890
Period size: 222 Copynumber: 2.0 Consensus size: 222
1115965 TCAAAGATAT
1115975 TGGATAATCTCAAAGTAGAGGAATACGGATCTTCAGTATACCGATAGATATCGGAATTCAGAATC
1 TGGATAATCTCAAAGTAGAGGAATACGGATCTTCAGTATACCGATAGATATCGGAATTCAGAATC
1116040 ACTATTGGAAGAGTTCAATGACTGACAGAATATCAGTTATTCAGAATGTGACTTGAGCTGATAAG
66 ACTATTGGAAGAGTTCAATGACTGACAGAATATCAGTTATTCAGAATGTGACTTGAGCTGATAAG
1116105 GAAGAAATGAAGGTTCATGACATTTATATTCTATGTCGATTGATCGGATTATCAACAACTCTTAC
131 GAAGAAATGAAGGTTCATGACATTTATATTCTATGTCGATTGATCGGATTATCAACAACTCTTAC
1116170 ATGAATAGTTCCCATAACTAATGCATG
196 ATGAATAGTTCCCATAACTAATGCATG
1116197 TGGATAATCTCAAAGTAGAGGAATACGGATCTTCAGTATACCGATAGATATCGGAATTCAGAATC
1 TGGATAATCTCAAAGTAGAGGAATACGGATCTTCAGTATACCGATAGATATCGGAATTCAGAATC
1116262 ACTATTGGAAGAGTTCAATGACTGACAGAATATCAGTTATTCAGAATGTGACTTGAGCTGATAAG
66 ACTATTGGAAGAGTTCAATGACTGACAGAATATCAGTTATTCAGAATGTGACTTGAGCTGATAAG
1116327 GAAGAAATGAAGGTTCATGACATTTATATTCTATGTCGATTGATCGGATTATCAACAACTCTTAC
131 GAAGAAATGAAGGTTCATGACATTTATATTCTATGTCGATTGATCGGATTATCAACAACTCTTAC
1116392 ATGAATAGTTCCCATAACTAATGCATG
196 ATGAATAGTTCCCATAACTAATGCATG
1116419 T
1 T
1116420 TAGATCTTCC
Statistics
Matches: 223, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
222 223 1.00
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.30
Consensus pattern (222 bp):
TGGATAATCTCAAAGTAGAGGAATACGGATCTTCAGTATACCGATAGATATCGGAATTCAGAATC
ACTATTGGAAGAGTTCAATGACTGACAGAATATCAGTTATTCAGAATGTGACTTGAGCTGATAAG
GAAGAAATGAAGGTTCATGACATTTATATTCTATGTCGATTGATCGGATTATCAACAACTCTTAC
ATGAATAGTTCCCATAACTAATGCATG
Found at i:1119868 original size:23 final size:22
Alignment explanation
Indices: 1119838--1119936 Score: 74
Period size: 23 Copynumber: 4.4 Consensus size: 22
1119828 CCACAATGCG
*
1119838 TATAAAATGCACCGAAGTGTCA
1 TATAAAATGCACCGAAGTGCCA
* * *
1119860 TATAGAAATGCACTGAAGTGTCG
1 TATA-AAATGCACCGAAGTGCCA
* * *
1119883 TGTAAAAATGCACCAAAATGCCA
1 TAT-AAAATGCACCGAAGTGCCA
*
1119906 TATAAAATGTC-CCGAAGGGCCA
1 TATAAAATG-CACCGAAGTGCCA
*
1119928 CATAGAAAT
1 TATA-AAAT
1119937 CTCTTTAAGA
Statistics
Matches: 60, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
22 21 0.35
23 38 0.63
24 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.21
Consensus pattern (22 bp):
TATAAAATGCACCGAAGTGCCA
Found at i:1120039 original size:21 final size:20
Alignment explanation
Indices: 1119964--1120040 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 20
1119954 ATATATATTA
* * *
1119964 CAAAGGACCAAATATGTGTCA
1 CAAA-GACCACATATATGTCC
1119985 CAAAGATCCACATATATGTTCC
1 CAAAGA-CCACATATATG-TCC
* **
1120007 CAAGGATTACATATATGTCC
1 CAAAGACCACATATATGTCC
1120027 CGAAAGACCACATA
1 C-AAAGACCACATA
1120041 GAACCCTCGA
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
20 6 0.14
21 31 0.70
22 7 0.16
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.22
Consensus pattern (20 bp):
CAAAGACCACATATATGTCC
Found at i:1124155 original size:21 final size:21
Alignment explanation
Indices: 1124131--1124210 Score: 101
Period size: 21 Copynumber: 3.7 Consensus size: 21
1124121 AAAGTGCCAT
1124131 AGTACACAAAGTACTACTACA
1 AGTACACAAAGTACTACTACA
1124152 AGTACACAAAGTACT-CTTGTA-A
1 AGTACACAAAGTACTAC---TACA
*
1124174 TAGTACACAAAGTACTACTCCA
1 -AGTACACAAAGTACTACTACA
1124196 AGTACACAAAGTACT
1 AGTACACAAAGTACT
1124211 CTTACGAAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 12
0.80 0.02 0.18
Matches are distributed among these distances:
20 1 0.02
21 31 0.60
22 2 0.04
23 17 0.33
24 1 0.02
ACGTcount: A:0.44, C:0.23, G:0.11, T:0.23
Consensus pattern (21 bp):
AGTACACAAAGTACTACTACA
Found at i:1124192 original size:44 final size:44
Alignment explanation
Indices: 1124129--1124213 Score: 161
Period size: 44 Copynumber: 1.9 Consensus size: 44
1124119 ACAAAGTGCC
1124129 ATAGTACACAAAGTACTACTACAAGTACACAAAGTACTCTTGTA
1 ATAGTACACAAAGTACTACTACAAGTACACAAAGTACTCTTGTA
*
1124173 ATAGTACACAAAGTACTACTCCAAGTACACAAAGTACTCTT
1 ATAGTACACAAAGTACTACTACAAGTACACAAAGTACTCTT
1124214 ACGAAAATGC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.25
Consensus pattern (44 bp):
ATAGTACACAAAGTACTACTACAAGTACACAAAGTACTCTTGTA
Found at i:1126404 original size:5 final size:5
Alignment explanation
Indices: 1126358--1126400 Score: 77
Period size: 5 Copynumber: 8.6 Consensus size: 5
1126348 CTTATCTTAC
*
1126358 ATAAG ATAAG ATAAG ATAAG ATAAG ATAAG ATAAG ATATG ATA
1 ATAAG ATAAG ATAAG ATAAG ATAAG ATAAG ATAAG ATAAG ATA
1126401 TGATGAGACT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.23
Consensus pattern (5 bp):
ATAAG
Found at i:1140069 original size:59 final size:59
Alignment explanation
Indices: 1139924--1140108 Score: 200
Period size: 60 Copynumber: 3.1 Consensus size: 59
1139914 TCTCGATTCC
* * * *
1139924 AAACTTCTAAACATTCCAAATTCATCCTCAAACTAT-ATCT-TTTGGTTAAAATTGGA-CCCT
1 AAACTTTTAAACATTCCAAATTCATCCTCAAATTATGATCTCATT--CT-AAATT-GATCCCT
* ** *
1139984 AAATTTTTAAACATTTTAATTTCATCCTCAAATTATGAATCTCATTCTAAATTGATCCC-
1 AAACTTTTAAACATTCCAAATTCATCCTCAAATTATG-ATCTCATTCTAAATTGATCCCT
* *
1140043 AAACTTTTAAACATTCCAAATTCATCCTCAAATTATGA-CTCATTCTAAGTTGGTCCCT
1 AAACTTTTAAACATTCCAAATTCATCCTCAAATTATGATCTCATTCTAAATTGATCCCT
1140101 AAACTTTT
1 AAACTTTT
1140109 CCATGTTCTA
Statistics
Matches: 106, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
57 17 0.16
58 9 0.08
59 35 0.33
60 38 0.36
61 1 0.01
62 4 0.04
63 2 0.02
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.38
Consensus pattern (59 bp):
AAACTTTTAAACATTCCAAATTCATCCTCAAATTATGATCTCATTCTAAATTGATCCCT
Found at i:1140363 original size:20 final size:20
Alignment explanation
Indices: 1140338--1140390 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1140328 GACCAACAAA
1140338 TTCGCAACGCGAACTCCAAT
1 TTCGCAACGCGAACTCCAAT
* **
1140358 TTCGCAAC-CTAGTTTCCAAT
1 TTCGCAACGCGA-ACTCCAAT
1140378 TTCGCAACGCGAA
1 TTCGCAACGCGAA
1140391 TCTGTAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.28, C:0.32, G:0.15, T:0.25
Consensus pattern (20 bp):
TTCGCAACGCGAACTCCAAT
Found at i:1140424 original size:20 final size:20
Alignment explanation
Indices: 1140396--1140486 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
1140386 GCGAATCTGT
1140396 AAATT-GCAACACAGAAGTC
1 AAATTCGCAACACAGAAGTC
*
1140415 AAATTCGCAACGC-GATAGTC
1 AAATTCGCAACACAGA-AGTC
*
1140435 AAATTCGCAACACAAAAGTC
1 AAATTCGCAACACAGAAGTC
* * * *
1140455 AGATTCGCAACGCGGAATTTC
1 AAATTCGCAACACAGAA-GTC
1140476 AAATTCGCAAC
1 AAATTCGCAAC
1140487 TGAATTTCAA
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
19 7 0.12
20 39 0.66
21 13 0.22
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.19
Consensus pattern (20 bp):
AAATTCGCAACACAGAAGTC
Found at i:1140505 original size:40 final size:40
Alignment explanation
Indices: 1140378--1140486 Score: 125
Period size: 40 Copynumber: 2.7 Consensus size: 40
1140368 AGTTTCCAAT
* *
1140378 TTCGCAACGCGAATCTGT-AAATT-GCAACACAGAAGTCAAA
1 TTCGCAACGCG-AT-AGTCAAATTCGCAACACAAAAGTCAAA
*
1140418 TTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAGA
1 TTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAA
*
1140458 TTCGCAACGCGGA-ATTTCAAATTCGCAAC
1 TTCGCAACGC-GATA-GTCAAATTCGCAAC
1140487 TGAATTTCAA
Statistics
Matches: 61, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
38 2 0.03
39 7 0.11
40 37 0.61
41 15 0.25
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (40 bp):
TTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAA
Found at i:1140519 original size:20 final size:19
Alignment explanation
Indices: 1140469--1140544 Score: 84
Period size: 19 Copynumber: 3.9 Consensus size: 19
1140459 TCGCAACGCG
1140469 GAATTTCAAATTCGCAACT
1 GAATTTCAAATTCGCAACT
1140488 GAATTTCAAATTCGCAACT
1 GAATTTCAAATTCGCAACT
* *
1140507 -ATATTTTCGAATTCGCAACAC
1 GA-A-TTTCAAATTCGCAAC-T
*
1140528 GAATTT-AATTTCGCAAC
1 GAATTTCAAATTCGCAAC
1140545 AGGTTTTAGT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
18 1 0.02
19 29 0.59
20 17 0.35
21 1 0.02
22 1 0.02
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.33
Consensus pattern (19 bp):
GAATTTCAAATTCGCAACT
Found at i:1140545 original size:19 final size:19
Alignment explanation
Indices: 1140518--1140564 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
1140508 TATTTTCGAA
1140518 TTCGCAACACGAATTTAAT
1 TTCGCAACACGAATTTAAT
** *
1140537 TTCGCAACA-GGTTTTAGT
1 TTCGCAACACGAATTTAAT
1140555 TTCGCAACAC
1 TTCGCAACAC
1140565 AAATGTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (19 bp):
TTCGCAACACGAATTTAAT
Found at i:1141354 original size:12 final size:12
Alignment explanation
Indices: 1141333--1141366 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1141323 ACCACATTTC
*
1141333 CAATAACAAACA
1 CAATATCAAACA
1141345 CAATATCAAACA
1 CAATATCAAACA
*
1141357 CAATCTCAAA
1 CAATATCAAA
1141367 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.59, C:0.26, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1141519 original size:24 final size:24
Alignment explanation
Indices: 1141492--1141545 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1141482 GTATTCGAAA
1141492 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1141516 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1141540 TTTGAT
1 TTTGAT
1141546 GATGTGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1144657 original size:24 final size:24
Alignment explanation
Indices: 1144606--1144658 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
1144596 TTTCATATGT
* * *
1144606 AATTGGAGTTTGAATTTCAATTTC
1 AATTTGAGTTTGAATTTCAATATA
1144630 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTCAATATA
1144654 AATTT
1 AATTT
1144659 CAGCTCCACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTCAATATA
Found at i:1145643 original size:18 final size:18
Alignment explanation
Indices: 1145620--1145655 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1145610 AAGCAAAAGG
1145620 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
1145638 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
1145656 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:1145980 original size:28 final size:28
Alignment explanation
Indices: 1145948--1146001 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
1145938 ATAATTCTTA
*
1145948 TTTACACATCAAATTAAACAAATCAACT
1 TTTACAAATCAAATTAAACAAATCAACT
* **
1145976 TTTACAAATCAACTTTTACAAATCAA
1 TTTACAAATCAAATTAAACAAATCAA
1146002 TTAAACAAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.31
Consensus pattern (28 bp):
TTTACAAATCAAATTAAACAAATCAACT
Found at i:1145982 original size:14 final size:14
Alignment explanation
Indices: 1145965--1146001 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
1145955 ATCAAATTAA
1145965 ACAAATCAACTTTT
1 ACAAATCAACTTTT
1145979 ACAAATCAACTTTT
1 ACAAATCAACTTTT
1145993 ACAAATCAA
1 ACAAATCAA
1146002 TTAAACAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1146931 original size:21 final size:21
Alignment explanation
Indices: 1146869--1146981 Score: 75
Period size: 21 Copynumber: 5.4 Consensus size: 21
1146859 ATGAATCGGG
* * *
1146869 CTCTTGAACGGCGGGCGGGAC
1 CTCTTGAACGGTGGGAGGGGC
** ** *
1146890 CTCTTGAACGAAGACATGGGC
1 CTCTTGAACGGTGGGAGGGGC
1146911 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
* * * *
1146932 TTCTTCG-ATGATGAGAGGGGC
1 CTCTT-GAACGGTGGGAGGGGC
* *
1146953 CTCTTGAACGGTAGGAGGCGC
1 CTCTTGAACGGTGGGAGGGGC
*
1146974 CTATTGAA
1 CTCTTGAA
1146982 TGATGATAGG
Statistics
Matches: 67, Mismatches: 23, Indels: 4
0.71 0.24 0.04
Matches are distributed among these distances:
20 1 0.01
21 65 0.97
22 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.37, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:1146985 original size:42 final size:42
Alignment explanation
Indices: 1146907--1146987 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
1146897 ACGAAGACAT
* * * *
1146907 GGGCCTCTTGAACGGTGGGAGGGGCTTCTTCGATGATGAGAG
1 GGGCCTCTTGAACGGTAGGAGGCGCCTATTCGATGATGAGAG
1146949 GGGCCTCTTGAACGGTAGGAGGCGCCTATT-GAATGATGA
1 GGGCCTCTTGAACGGTAGGAGGCGCCTATTCG-ATGATGA
1146988 TAGGTGCATC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 1 0.03
42 33 0.97
ACGTcount: A:0.20, C:0.17, G:0.40, T:0.23
Consensus pattern (42 bp):
GGGCCTCTTGAACGGTAGGAGGCGCCTATTCGATGATGAGAG
Found at i:1149156 original size:19 final size:19
Alignment explanation
Indices: 1149105--1149158 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
1149095 AGTAGTTTCT
*
1149105 GAAACTTAAATTCGCAACGC
1 GAAAC-TAAAATCGCAACGC
*
1149125 GAAAATGAAAATCGCAACGC
1 GAAACT-AAAATCGCAACGC
1149145 GAAACTAAAATCGC
1 GAAACTAAAATCGC
1149159 GTTGCGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.30
20 21 0.70
ACGTcount: A:0.46, C:0.22, G:0.17, T:0.15
Consensus pattern (19 bp):
GAAACTAAAATCGCAACGC
Found at i:1149194 original size:20 final size:21
Alignment explanation
Indices: 1149165--1149203 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1149155 TCGCGTTGCG
*
1149165 ATTTTGGTGTTGC-AATTTTC
1 ATTTTCGTGTTGCGAATTTTC
1149185 ATTTTCGTGTTGCGAATTT
1 ATTTTCGTGTTGCGAATTT
1149204 AAGTTTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.21, T:0.54
Consensus pattern (21 bp):
ATTTTCGTGTTGCGAATTTTC
Found at i:1149600 original size:22 final size:22
Alignment explanation
Indices: 1149545--1149602 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
1149535 GATGGAGATA
*
1149545 GACGGATTTCGCCGGAGACGGG
1 GACGGATTTCGTCGGAGACGGG
*
1149567 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGACGGG
*
1149589 GACGGATGTCGTCG
1 GACGGATTTCGTCG
1149603 TAGAGAGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.17, C:0.19, G:0.45, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGACGGG
Found at i:1149761 original size:20 final size:20
Alignment explanation
Indices: 1149732--1149962 Score: 207
Period size: 20 Copynumber: 11.6 Consensus size: 20
1149722 GAAATTCCGC
*
1149732 GTTGCAAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* * ***
1149752 GTTGCGAATTTGGCTATCAC
1 GTTGCGAATTTGACTTTTGT
* *
1149772 GTTGTGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTTTGT
* *
1149792 G-CGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTTTGT
1149811 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* * * *
1149831 GTTGTGAATTTGACTATCGC
1 GTTGCGAATTTGACTTTTGT
1149851 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* ***
1149871 GTTGCG-ATTT-ACAAATTCAC
1 GTTGCGAATTTGAC--TTTTGT
* * * *
1149891 GTTGCGAATCTGACTATCGC
1 GTTGCGAATTTGACTTTTGT
1149911 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* *
1149931 GTTGCGAATTTGACTATTGC
1 GTTGCGAATTTGACTTTTGT
1149951 GTTGCGAATTTG
1 GTTGCGAATTTG
1149963 GAAAACCGCA
Statistics
Matches: 167, Mismatches: 39, Indels: 10
0.77 0.18 0.05
Matches are distributed among these distances:
18 2 0.01
19 21 0.13
20 139 0.83
21 3 0.02
22 2 0.01
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.42
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:1149784 original size:40 final size:40
Alignment explanation
Indices: 1149711--1149962 Score: 244
Period size: 40 Copynumber: 6.3 Consensus size: 40
1149701 TGTGTTTCGC
* *
1149711 GTTGCGAATTTGA-AATTCCGCGTTGCAAATTTGACTTTTGT
1 GTTGCGAATTTGACTA-T-CGCGTTGCGAATTTGACTTTTGT
* * * *
1149752 GTTGCGAATTTGGCTATCACGTTGTGAATTTGACTTCTGT
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGT
* *
1149792 G-CGCGAATTTGACT-TCTGTGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTATC-GCGTTGCGAATTTGACTTTTGT
*
1149831 GTTGTGAATTTGACTATCGCGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGT
* * * * * *
1149871 GTTGCG-ATTT-ACAAATTCACGTTGCGAATCTGACTATCGC
1 GTTGCGAATTTGAC-TA-TCGCGTTGCGAATTTGACTTTTGT
* * * * *
1149911 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATTGC
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGT
1149951 GTTGCGAATTTG
1 GTTGCGAATTTG
1149963 GAAAACCGCA
Statistics
Matches: 174, Mismatches: 29, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
38 4 0.02
39 35 0.20
40 113 0.65
41 19 0.11
42 3 0.02
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.42
Consensus pattern (40 bp):
GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGT
Found at i:1149826 original size:79 final size:80
Alignment explanation
Indices: 1149714--1149945 Score: 236
Period size: 79 Copynumber: 2.9 Consensus size: 80
1149704 GTTTCGCGTT
* *
1149714 GCGAATTTGAAATTCCGCGTTGCAAATTTGACTTTTGTGTTGCGAATTTGGCTATCACGTTGTGA
1 GCGAATTTGAAATTCCGCGTTGCAAATTTGACTTTTGTGTTGCGAATTTGACTATCACGTTGCGA
1149779 ATTTGACTTCTGTGC
66 ATTTGACTTCTGTGC
* * * * * *
1149794 GCGAATTTG-ACTTCTGTGTTGCGAATTTGACTTTTGTGTTGTGAATTTGACTATCGCGTTGCGA
1 GCGAATTTGAAATTCCGCGTTGCAAATTTGACTTTTGTGTTGCGAATTTGACTATCACGTTGCGA
* *
1149858 ATTTGACTTTTGTGTT
66 ATTTGACTTCTGTG-C
* * * * * * * * ***
1149874 GCG-ATTTACAAATT-CACGTTGCGAATCTGACTATCGCGTTGCGAATTTGACTTTTGTGTTGCG
1 GCGAATTT-GAAATTCCGCGTTGCAAATTTGACTTTTGTGTTGCGAATTTGACTATCACGTTGCG
1149937 AATTTGACT
65 AATTTGACT
1149946 ATTGCGTTGC
Statistics
Matches: 126, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
79 64 0.51
80 59 0.47
81 3 0.02
ACGTcount: A:0.19, C:0.16, G:0.24, T:0.41
Consensus pattern (80 bp):
GCGAATTTGAAATTCCGCGTTGCAAATTTGACTTTTGTGTTGCGAATTTGACTATCACGTTGCGA
ATTTGACTTCTGTGC
Found at i:1149905 original size:60 final size:60
Alignment explanation
Indices: 1149729--1149962 Score: 264
Period size: 60 Copynumber: 3.9 Consensus size: 60
1149719 TTTGAAATTC
* *
1149729 CGCGTTGCAAATTTGACTTTTGTGTTGCGAATTTGGC-TATCACGTTGTGAATTTGACT-T
1 CGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACAT-TCACGTTGTGAATTTGACTAT
* * * * ***
1149788 C-TGTGCGCGAATTTGACTTCTGTGTTGCGAATTTGACTTTTGTGTTGTGAATTTGACTAT
1 CGCGT-TGCGAATTTGACTTTTGTGTTGCGAATTTGACATTCACGTTGTGAATTTGACTAT
* *
1149848 CGCGTTGCGAATTTGACTTTTGTGTTGCG-ATTT-ACAAATTCACGTTGCGAATCTGACTAT
1 CGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGAC--ATTCACGTTGTGAATTTGACTAT
* *
1149908 CGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATT-GCGTTGCGAATTTG
1 CGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGAC-ATTCACGTTGTGAATTTG
1149963 GAAAACCGCA
Statistics
Matches: 147, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
58 4 0.03
59 49 0.33
60 83 0.56
61 9 0.06
62 2 0.01
ACGTcount: A:0.18, C:0.15, G:0.24, T:0.42
Consensus pattern (60 bp):
CGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACATTCACGTTGTGAATTTGACTAT
Found at i:1150041 original size:21 final size:21
Alignment explanation
Indices: 1149954--1150030 Score: 154
Period size: 21 Copynumber: 3.7 Consensus size: 21
1149944 CTATTGCGTT
1149954 GCGAATTTGGAAAACCGCAAC
1 GCGAATTTGGAAAACCGCAAC
1149975 GCGAATTTGGAAAACCGCAAC
1 GCGAATTTGGAAAACCGCAAC
1149996 GCGAATTTGGAAAACCGCAAC
1 GCGAATTTGGAAAACCGCAAC
1150017 GCGAATTTGGAAAA
1 GCGAATTTGGAAAA
1150031 TTGCAATGCG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.16
Consensus pattern (21 bp):
GCGAATTTGGAAAACCGCAAC
Found at i:1150098 original size:20 final size:19
Alignment explanation
Indices: 1150049--1150102 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
1150039 CGATTTACAT
1150049 ATTCGCGTTGCGAAATTGG
1 ATTCGCGTTGCGAAATTGG
** *
1150068 AAACTGGGTTGCGAAATTGG
1 ATTC-GCGTTGCGAAATTGG
1150088 AGTTCGCGTTGCGAA
1 A-TTCGCGTTGCGAA
1150103 TTTGTTGGTC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 24 0.89
21 1 0.04
ACGTcount: A:0.24, C:0.15, G:0.33, T:0.28
Consensus pattern (19 bp):
ATTCGCGTTGCGAAATTGG
Found at i:1150753 original size:2 final size:2
Alignment explanation
Indices: 1150746--1150805 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
1150736 GAATTATTGA
1150746 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1150788 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
1150806 TGTTTTTGAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1151108 original size:2 final size:2
Alignment explanation
Indices: 1151101--1151139 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1151091 ACTTAAACAT
1151101 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1151140 TGAAATAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1155641 original size:445 final size:450
Alignment explanation
Indices: 1154806--1155646 Score: 1417
Period size: 445 Copynumber: 1.9 Consensus size: 450
1154796 TCACTAAAGG
*
1154806 TGTTGGGTTATGGGGTCCAGCGATCACCCTTAGAGATTCTATTGTATATGGGCGCGATATTGGTG
1 TGTTGGGTTATGGGGTCCAGCGATCACCCTTAGAGATTCTATCGTATATGGGCGCGATATTGGTG
1154871 CGTGACTGCCCAACCCGCCGAGGCCCACGTGTGCCTTGCGAAGCCCCTAGGCCCGCCCGCAGCAC
66 CGTGACTGCCCAACCCGCCGAGGCCCACGTGTGCCTTGCGAAGCCCCTAGGCCCGCCCGCAG-AC
* * *
1154936 GCTATAGATGCGGGGCTCCGCAATACCGTGGTGAATTGTGGGGGGGTGCCCCACAAGAATCCATC
130 GCTATAGATGCGGGGCTCCGCAATACCGTGATGAACTGTGGGGGGGTGCCCCACAAGAATCCACC
* * *
1155001 TTGGCTTGGGGGAATCCAGCGATCACTCACTACAAAGATATGAGGTTAAAATGGCTCACTTACTT
195 TTGGCTTGGGGGAATCCAGCGATCACTCACTACAAAGATATGAGGTTAAAATGACCCACCTACTT
*
1155066 ATCACCAATTGGTTTTAAGAAGGAATGGTGACCATTCGCTTCATAACTCTGTAGTTAAGCGTGCT
260 ATCACCAATTGGTTTTAAGAAGGAATGGTGACCATTCGCTTCAGAACTCTGTAGTTAAGCGTGCT
* *
1155131 TGGACCAGGGAAATCGAAGGATGGGTGAGCCACTGGGAAGTTGTTCAGAAATGAATGATTCGATC
325 TGGACCAGGAAAATCCAAGGATGGGTGAGCCACTGGGAAGTTGTTCAGAAATGAATGATTCGATC
1155196 CTACAATTAGTATCAGAGCAGGTTGCAGGTTCGAATCCCCCAGGTGTCGCTGGGGGGTGAT
390 CTACAATTAGTATCAGAGCAGGTTGCAGGTTCGAATCCCCCAGGTGTCGCTGGGGGGTGAT
*
1155257 TGTTGGGTTATGGGGTCCAGCGATCACCCTTAGAGATTCTATCGTGTATGGGCGCGATATTGGTG
1 TGTTGGGTTATGGGGTCCAGCGATCACCCTTAGAGATTCTATCGTATATGGGCGCGATATTGGTG
* * * *
1155322 CGTGACTGCCCAATCTGTCGAGGCCCACGTGTGCCTTGCGAAGCCCCTAGGCTCG-CC-C-G-CG
66 CGTGACTGCCCAACCCGCCGAGGCCCACGTGTGCCTTGCGAAGCCCCTAGGCCCGCCCGCAGACG
* ** *
1155383 CTATAGATGCGGGGCTCTGCAATGTCGTGATGAACTGT-GGGGGGTGCCCCACAATAATCCACCT
131 CTATAGATGCGGGGCTCCGCAATACCGTGATGAACTGTGGGGGGGTGCCCCACAAGAATCCACCT
*
1155447 TGGCTTGGGGGAA-CTCAGTGATCACTCACTACAAAGATATGAGGTTAAAATGACCCACCTACTT
196 TGGCTTGGGGGAATC-CAGCGATCACTCACTACAAAGATATGAGGTTAAAATGACCCACCTACTT
1155511 ATCACCAATTGGTTTTAAGAAGGAATGGTGACCATTCGCTTCAGAACTCTGTAGTTAAGCGTGCT
260 ATCACCAATTGGTTTTAAGAAGGAATGGTGACCATTCGCTTCAGAACTCTGTAGTTAAGCGTGCT
*
1155576 TGGATCAGGAAAATCCAAGGATGGGTG-GCCCACTGGGAAGTTGTTCAGAAATGAATGATTCGAT
325 TGGACCAGGAAAATCCAAGGATGGGTGAG-CCACTGGGAAGTTGTTCAGAAATGAATGATTCGAT
1155640 CCTACAA
389 CCTACAA
1155647 AAGGTTTAAA
Statistics
Matches: 367, Mismatches: 21, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
444 2 0.01
445 212 0.58
446 35 0.10
448 1 0.00
449 1 0.00
450 2 0.01
451 114 0.31
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.25
Consensus pattern (450 bp):
TGTTGGGTTATGGGGTCCAGCGATCACCCTTAGAGATTCTATCGTATATGGGCGCGATATTGGTG
CGTGACTGCCCAACCCGCCGAGGCCCACGTGTGCCTTGCGAAGCCCCTAGGCCCGCCCGCAGACG
CTATAGATGCGGGGCTCCGCAATACCGTGATGAACTGTGGGGGGGTGCCCCACAAGAATCCACCT
TGGCTTGGGGGAATCCAGCGATCACTCACTACAAAGATATGAGGTTAAAATGACCCACCTACTTA
TCACCAATTGGTTTTAAGAAGGAATGGTGACCATTCGCTTCAGAACTCTGTAGTTAAGCGTGCTT
GGACCAGGAAAATCCAAGGATGGGTGAGCCACTGGGAAGTTGTTCAGAAATGAATGATTCGATCC
TACAATTAGTATCAGAGCAGGTTGCAGGTTCGAATCCCCCAGGTGTCGCTGGGGGGTGAT
Found at i:1161572 original size:36 final size:36
Alignment explanation
Indices: 1161513--1161581 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
1161503 TTTCGGTGGG
* *
1161513 GTGATGGGGGTTAGGTTTCCTTTTTTTTAATATTGAA
1 GTGATGGGGGTTAGGTTTACTTTTTCTT-ATATTGAA
1161550 GTGATGGGGG-TAGGTTTACTTTTTCTTATATT
1 GTGATGGGGGTTAGGTTTACTTTTTCTTATATT
1161582 TATTATGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 5 0.17
36 15 0.50
37 10 0.33
ACGTcount: A:0.17, C:0.06, G:0.28, T:0.49
Consensus pattern (36 bp):
GTGATGGGGGTTAGGTTTACTTTTTCTTATATTGAA
Found at i:1161718 original size:4 final size:4
Alignment explanation
Indices: 1161693--1161738 Score: 56
Period size: 4 Copynumber: 11.0 Consensus size: 4
1161683 ACCTTTCTTC
* *
1161693 TTTA TCTTA TCTTA TCTA TTTA TTTA TTTA TTTA ATTA TTTA TTTA
1 TTTA T-TTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1161739 GTTTTCTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
4 28 0.76
5 9 0.24
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:1162819 original size:14 final size:14
Alignment explanation
Indices: 1162802--1162828 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1162792 CTTTACCATT
1162802 TTTTTATTTATTTA
1 TTTTTATTTATTTA
1162816 TTTTTATTTATTT
1 TTTTTATTTATTT
1162829 CTATTTTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTATTTATTTA
Found at i:1171915 original size:6 final size:6
Alignment explanation
Indices: 1171900--1171932 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1171890 TCCTAAGTTG
*
1171900 AAAA-A AAAACA AAAACA AAAATA AAAACA AAAA
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAAA
1171933 AATAGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.88, C:0.09, G:0.00, T:0.03
Consensus pattern (6 bp):
AAAACA
Found at i:1171941 original size:21 final size:22
Alignment explanation
Indices: 1171917--1171965 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
1171907 AACAAAAACA
*
1171917 AAAATAAA-AACAAAAAAATAG
1 AAAATAAAGAACAAAAAAAGAG
* *
1171938 AAAA-AAAGAACGAAAGAAGAG
1 AAAATAAAGAACAAAAAAAGAG
1171959 AAAATAA
1 AAAATAA
1171966 GGGGGGTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 3 0.13
21 18 0.78
22 2 0.09
ACGTcount: A:0.78, C:0.04, G:0.12, T:0.06
Consensus pattern (22 bp):
AAAATAAAGAACAAAAAAAGAG
Found at i:1172957 original size:105 final size:105
Alignment explanation
Indices: 1172699--1173475 Score: 1241
Period size: 105 Copynumber: 7.4 Consensus size: 105
1172689 AGGTTTTACC
* * *
1172699 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * *
1172764 ACGAAGAGACCGCTGGTTGTCAATAAACAACTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
* *
1172805 CATAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCATACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1172870 ACGAAGGGACCGCTGGTTGTCAACAAACATCTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
1172910 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1172975 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
1173015 CAGAGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAATTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
1173080 ACGAAGGGACCGCTGGTTGTCAATAAATATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
1173120 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
1173185 ACGAAGGGACCGCTGGTTGTCAACAAGCATCTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
1173225 CAGAGCCAATTTCAACTTCACAAAGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1173290 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* * *
1173330 CAGAGCCAATTTCAACTCCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
1173395 ACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCCCAGTTC
66 ACGAAGGGACCG-CTGGTTGTCAACAAAC-ATTTCTCAATTT
* * *** *
1173436 CAGAACCAATTTCAACTCCACGGTGGAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1173476 GGAACAATAC
Statistics
Matches: 629, Mismatches: 40, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
104 2 0.00
105 497 0.79
106 130 0.21
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:1175547 original size:35 final size:36
Alignment explanation
Indices: 1175489--1175556 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 36
1175479 TTTCGGTGGG
* *
1175489 GTGATGGGGGGTAGGTTTCCTTTTT-TTAATATTGAA
1 GTGATGGGAGGTAGGTTTACTTTTTCTT-ATATTGAA
1175525 GTGAT-GGAGGTAGGTTTACTTTTTCTTATATT
1 GTGATGGGAGGTAGGTTTACTTTTTCTTATATT
1175557 TATTATGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
35 22 0.76
36 7 0.24
ACGTcount: A:0.19, C:0.06, G:0.28, T:0.47
Consensus pattern (36 bp):
GTGATGGGAGGTAGGTTTACTTTTTCTTATATTGAA
Found at i:1175693 original size:4 final size:4
Alignment explanation
Indices: 1175668--1175713 Score: 56
Period size: 4 Copynumber: 11.0 Consensus size: 4
1175658 ACCTTTCTTC
* *
1175668 TTTA TCTTA TCTTA TCTA TTTA TTTA TTTA TTTA ATTA TTTA TTTA
1 TTTA T-TTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1175714 GTTTTCTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
4 28 0.76
5 9 0.24
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:1184131 original size:60 final size:60
Alignment explanation
Indices: 1184046--1184169 Score: 140
Period size: 60 Copynumber: 2.1 Consensus size: 60
1184036 TATTCATTCT
* ** * *** *
1184046 CAAACTAGGATTCTCATTGTAAATTGTTCTTTAAATTTTTGAATATTCCAATTTCATCCC
1 CAAACTAGGACTCTCATTCCAAATTGATCCCCAAACTTTTGAATATTCCAATTTCATCCC
* * * *
1184106 CAAACTATGACTCTCATTCCAAATTGATCCCCAAACTTTTGAATCTTCCTATTTCATCCT
1 CAAACTAGGACTCTCATTCCAAATTGATCCCCAAACTTTTGAATATTCCAATTTCATCCC
1184166 CAAA
1 CAAA
1184170 TTCATCCAAA
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.31, C:0.24, G:0.06, T:0.39
Consensus pattern (60 bp):
CAAACTAGGACTCTCATTCCAAATTGATCCCCAAACTTTTGAATATTCCAATTTCATCCC
Found at i:1186637 original size:34 final size:34
Alignment explanation
Indices: 1186594--1186663 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
1186584 TTTCGTCCTA
1186594 TTAGGATTCAAACTCCTAAAAATAAGATAGAATT
1 TTAGGATTCAAACTCCTAAAAATAAGATAGAATT
* *
1186628 TTAGGATTCAAACTCCTAAAGATATGATAGAATT
1 TTAGGATTCAAACTCCTAAAAATAAGATAGAATT
1186662 TT
1 TT
1186664 GCTAAGATTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (34 bp):
TTAGGATTCAAACTCCTAAAAATAAGATAGAATT
Found at i:1187117 original size:18 final size:17
Alignment explanation
Indices: 1187078--1187120 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1187068 ATTATATGGA
1187078 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
1187094 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
1187112 TATTATTAT
1 TATTATTAT
1187121 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:1190022 original size:8 final size:8
Alignment explanation
Indices: 1190009--1190047 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
1189999 GAACATTTCA
*
1190009 TGCATTCT
1 TGCATTTT
1190017 TGCA-TTT
1 TGCATTTT
1190024 TGCATTTT
1 TGCATTTT
*
1190032 TGCCTTTT
1 TGCATTTT
1190040 TGCATTTT
1 TGCATTTT
1190048 CATCTACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (8 bp):
TGCATTTT
Found at i:1191198 original size:22 final size:22
Alignment explanation
Indices: 1191175--1191236 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
1191165 CAAAAAGGGC
1191175 AAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAGAAAAAA-AAAAGAAGCA
* *
1191198 AAAAAGGAAAAAACAAGAA-CA
1 AAAAAGAAAAAAAAAAGAAGCA
1191219 AAAAAGAAAGAACAAAAA
1 AAAAAGAAA-AA-AAAAA
1191237 TAAAAAAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.30
22 8 0.24
23 15 0.45
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAAAAAAAGAAGCA
Found at i:1191227 original size:20 final size:20
Alignment explanation
Indices: 1191175--1191243 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 20
1191165 CAAAAAGGGC
*
1191175 AAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAG-AAAAA-ACAAGAA-CA
1191198 AAAAAGGAAAAAACAAGAACA
1 AAAAA-GAAAAAACAAGAACA
* * *
1191219 AAAAAGAAAGAACAAAAATA
1 AAAAAGAAAAAACAAGAACA
1191239 AAAAA
1 AAAAA
1191244 AAGGGACAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 17 0.41
21 7 0.17
22 6 0.15
23 10 0.24
24 1 0.02
ACGTcount: A:0.80, C:0.06, G:0.13, T:0.01
Consensus pattern (20 bp):
AAAAAGAAAAAACAAGAACA
Found at i:1191882 original size:22 final size:22
Alignment explanation
Indices: 1191854--1191904 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1191844 CCCCATTAAT
1191854 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
*
1191876 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
1191898 CCTTTGA
1 CCTTTGA
1191905 CCAAATGACC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:1191911 original size:19 final size:21
Alignment explanation
Indices: 1191854--1191911 Score: 75
Period size: 22 Copynumber: 2.8 Consensus size: 21
1191844 CCCCATTAAT
*
1191854 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCA-CAAATGCCAAA
1191876 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCA-CAAATGCCAAA
1191898 CCTTTGA-C-CAAATG
1 CCTTTGAGCACAAATG
1191912 ACCTGAAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
19 6 0.17
21 1 0.03
22 28 0.80
ACGTcount: A:0.36, C:0.28, G:0.12, T:0.24
Consensus pattern (21 bp):
CCTTTGAGCACAAATGCCAAA
Found at i:1192844 original size:37 final size:37
Alignment explanation
Indices: 1192759--1192868 Score: 177
Period size: 37 Copynumber: 3.0 Consensus size: 37
1192749 GTGCTCACTA
1192759 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
*
1192795 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
* *
1192832 TTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAC
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAAC
1192869 ATTGAAAACA
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
36 31 0.46
37 34 0.50
38 3 0.04
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
Found at i:1192953 original size:102 final size:102
Alignment explanation
Indices: 1192794--1193167 Score: 631
Period size: 102 Copynumber: 3.7 Consensus size: 102
1192784 TGAAACAAAC
** *
1192794 TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
1 TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTCCGTCTCCATTGAGACAGTTTCTCTTG
1192859 AAACATAAACATTGAAAACATTTCCCTTGAAATGAGT
66 AAACATAAACATTGAAAACATTTCCCTTGAAATGAGT
*
1192896 TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTCCGTCTCCATTGAGACAGTTTCTCTTG
1 TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTCCGTCTCCATTGAGACAGTTTCTCTTG
1192961 AAACATAAACATTGAAAACATTTCCCTTGAAATGAGT
66 AAACATAAACATTGAAAACATTTCCCTTGAAATGAGT
* *
1192998 TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTCCGTCTCCATTGAGATAGTTTCTCTTG
1 TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTCCGTCTCCATTGAGACAGTTTCTCTTG
*
1193063 AAACATAAACATTGAAAACATTTCCCTTGAAATGAAT
66 AAACATAAACATTGAAAACATTTCCCTTGAAATGAGT
* * ** *
1193100 TTCGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTTCTCTT
1 TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTCCGTCTCCATTGAGACAG-TTTCTCTT
1193165 GAA
65 GAA
1193168 GCATCATCTT
Statistics
Matches: 258, Mismatches: 13, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
102 247 0.96
103 11 0.04
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.37
Consensus pattern (102 bp):
TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTCCGTCTCCATTGAGACAGTTTCTCTTG
AAACATAAACATTGAAAACATTTCCCTTGAAATGAGT
Found at i:1193310 original size:37 final size:37
Alignment explanation
Indices: 1193240--1193311 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
1193230 TGGAACTAAG
* **
1193240 TTTTATCTCACTTGAGACAGTTTTTCTTAAAACAAAA
1 TTTTATCTCACTTAAGACAGTTTCCCTTAAAACAAAA
* * *
1193277 TTTTATCTCCCTTAAGACCGTTTCCCTTGAAACAA
1 TTTTATCTCACTTAAGACAGTTTCCCTTAAAACAA
1193312 CAAATATCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (37 bp):
TTTTATCTCACTTAAGACAGTTTCCCTTAAAACAAAA
Found at i:1193915 original size:105 final size:105
Alignment explanation
Indices: 1193772--1194659 Score: 891
Period size: 105 Copynumber: 8.5 Consensus size: 105
1193762 GAAGCCAAAC
* * *
1193772 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAATT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTT
* * * ** *
1193837 CAACTTCACGACGAAGGGACCGTTGCCTGTCAACAACAAC
66 CAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAAT
** *
1193877 TTCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACAAAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTT
*
1193942 CAACTTCACAACGAAGGGACGGCTGGTTGTCAACAATAAT
66 CAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAAT
* * *
1193982 TTC-CTAGTTTCAGGGCCAATTTCAACTTCACAGCGAAGGATATTGGAC-CCAAGACAGCACAAG
1 TTCTC-AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC-AGACAACACAAG
* * * ** *
1194045 CTCAACTTCACAGCGAAGGGGCGGCTGACTGT---CGACAA-
64 TTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAAT
* * * * *
1194083 ---GCAATTTCGGAGCCAATCTCAACTTCACAGCGAAGAATATTGGACTCGAGACAACACAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTT
*
1194145 CAACTTCACAGCGAAGGGACGGCTGGTTGTCAACAAACAAT
66 CAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AACAAT
* * * * *
1194186 TTCCCAATTCCAGAGCCGATTTCAACTCCAC-GAC-AGAGGATATCGTG-CTACCCGAGACAACA
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAG-CGA-AGGATATTG-GACT--CC-AGACAACA
1194248 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACT
60 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AACAA-T
* ** * * * * * *
1194296 TT-TCAGTTTCA-TCCGCGATTTTAACTCCAC-GACGGAGGATATCGTGCCACTCGAGACAACAC
1 TTCTCAATTTCAGAGC-CAATTTCAACTTCACAG-CGAAGGATAT--TG-GACTCCAGACAACAC
1194358 AAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAA-ACAT
61 AAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACA-AT
* * *
1194403 TTTTCAAATTTCAGAGCCAATTTCAACTTCGCAGCGAAGGATATTGGACTCGAGACAACACAAGT
1 TTCTC-AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGT
* *
1194468 TCAACTTCACAACGAAGGGACGGCTGATTGTCAACAA-GA-
65 TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAAT
* * * * * * *
1194507 TT-TC--GTTCAGAGTCAATTTCATCTTCACAGCGAAGGATATTAGACTCGAGACAGCACAAGCT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTT
* * **
1194569 CAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAAT
66 CAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AACAAT
* * * * *
1194610 TTCCCAGTTCCAGAACCAATTTCAACTTCACAGCGGAGGATATTGGACTC
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
1194660 GGAACAATAT
Statistics
Matches: 660, Mismatches: 88, Indels: 69
0.81 0.11 0.08
Matches are distributed among these distances:
98 77 0.12
99 2 0.00
100 82 0.12
101 3 0.00
102 9 0.01
103 4 0.01
104 6 0.01
105 176 0.27
106 122 0.18
107 7 0.01
108 7 0.01
109 156 0.24
110 6 0.01
111 1 0.00
112 2 0.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (105 bp):
TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTT
CAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAAT
Found at i:1194651 original size:424 final size:413
Alignment explanation
Indices: 1193776--1194659 Score: 1112
Period size: 424 Copynumber: 2.1 Consensus size: 413
1193766 CCAAACTTCT
* * * *
1193776 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAATTCAAC
1 CAATTCCAGAGCCAATTTCAACTTCACAGCGGAGGATATTGGACTCCAGACAACACAAATTCAAC
* * * *
1193841 TTCACGACGAAGGGACCGTTGCCTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTC
66 TTCACAACGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCACAGCCAATTTCAACTCC
* *
1193906 ACAATGAAGGATATTGGACTCCAGACAACAAAAGTTCAACTTCACAACGAAGGGACGGCTGGTTG
131 ACAACGAAGGATATTGCACTCCAGACAACAAAAGTTCAACTTCACAACGAAGGGACGGCTGGTTG
* * *
1193971 TCAACAATAATTTCCTAGTTTCAGGGCCAATTTCAACTTCACAGCGAAGGATATTGGACCCAAGA
196 TCAACAATAATTTCCAAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACCCAAGA
* * * *
1194036 CAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCGACAAGCAATTTCGGAGCCAATC
261 CAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAG-AATTTCGGAGCCAATC
* *
1194101 TCAACTTCACAGCGAAGAATATTGGACTCGAGACAACACAAGTTCAACTTCACAGCGAAGGGACG
325 TCAACTTCACAGCGAAGAATATTAGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGACG
**
1194166 GCTGGTTGTCAACAAACAATTTCC
390 GCTGACTGTCAACAAACAATTTCC
* * * * *
1194190 CAATTCCAGAGCCGATTTCAACTCCAC-GACAGAGGATATCGTG-CTACCCGAGACAACACAAGT
1 CAATTCCAGAGCCAATTTCAACTTCACAG-CGGAGGATATTG-GACT--CC-AGACAACACAAAT
* ** * * * *
1194253 TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTTTCAGTTTCATCCG-CGATTT
61 TCAACTTCACAACGAAGGGACCGCTGCCTGTCAAC-AACAACTTCTCAATTTCA-CAGCCAATTT
* * * * *
1194317 TAACTCCACGACGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA
124 CAACTCCACAACGAAGGATAT--TG-CACTCCAGACAACAAAAGTTCAACTTCACAACGAAGGGA
* *
1194382 CGGCTGGTTGTCAACAA-ACATTTTTCAAATTTCAGAGCCAATTTCAACTTCGCAGCGAAGGATA
186 CGGCTGGTTGTCAACAATA-A-TTTCCAAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATA
* * * *
1194446 TTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAG-ATTT
249 TTGGACCCAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAGAATTT
* * * * *
1194510 CGTTCAGAGTCAATTTCATCTTCACAGCGAAGGATATTAGACTCGAGACAGCACAAGCTCAACTT
314 CG----GAGCCAATCTCAACTTCACAGCGAAGAATATTAGACTCGAGACAACACAAGCTCAACTT
*
1194575 CACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCC
375 CACAGCGAAGGGACGGCTGACTGTCAACAAACAATTTCC
* *
1194614 CAGTTCCAGAACCAATTTCAACTTCACAGCGGAGGATATTGGACTC
1 CAATTCCAGAGCCAATTTCAACTTCACAGCGGAGGATATTGGACTC
1194660 GGAACAATAT
Statistics
Matches: 396, Mismatches: 56, Indels: 28
0.82 0.12 0.06
Matches are distributed among these distances:
414 35 0.09
415 1 0.00
416 2 0.01
417 41 0.10
418 37 0.09
419 1 0.00
420 9 0.02
421 54 0.14
422 91 0.23
423 1 0.00
424 123 0.31
425 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (413 bp):
CAATTCCAGAGCCAATTTCAACTTCACAGCGGAGGATATTGGACTCCAGACAACACAAATTCAAC
TTCACAACGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCACAGCCAATTTCAACTCC
ACAACGAAGGATATTGCACTCCAGACAACAAAAGTTCAACTTCACAACGAAGGGACGGCTGGTTG
TCAACAATAATTTCCAAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACCCAAGA
CAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAGAATTTCGGAGCCAATCT
CAACTTCACAGCGAAGAATATTAGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGACGG
CTGACTGTCAACAAACAATTTCC
Found at i:1195165 original size:34 final size:34
Alignment explanation
Indices: 1195122--1195245 Score: 125
Period size: 34 Copynumber: 3.8 Consensus size: 34
1195112 TTCGTCCTAC
1195122 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
*
1195156 TAGGATTCAAACTCCT-AAAATATGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * * *
1195189 T--G-CT-AAGA-TTCAAAAAATATGATAGAATTT
1 TAGGATTCAA-ACTCCTAAAAATAGGATAGAATTT
* * *
1195219 TATGATTTAAACTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
1195246 CCACAAGCAC
Statistics
Matches: 74, Mismatches: 9, Indels: 14
0.76 0.09 0.14
Matches are distributed among these distances:
29 4 0.05
30 20 0.27
31 1 0.01
32 1 0.01
33 19 0.26
34 29 0.39
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.32
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:1195630 original size:17 final size:18
Alignment explanation
Indices: 1195604--1195643 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1195594 ATTATATGGA
1195604 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
1195620 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
1195638 TATTAT
1 TATTAT
1195644 ATGTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:1195726 original size:28 final size:28
Alignment explanation
Indices: 1195681--1195735 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
1195671 TGATTTTTTA
*
1195681 ATATATTTTATTATTATTATTA-TTATAT
1 ATATATTTTATTAATATT-TTACTTATAT
1195709 ATATATTTCT-TTAATATTTTACTTATA
1 ATATATTT-TATTAATATTTTACTTATA
1195736 AGTCTAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 3 0.12
28 20 0.83
29 1 0.04
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (28 bp):
ATATATTTTATTAATATTTTACTTATAT
Found at i:1197581 original size:39 final size:39
Alignment explanation
Indices: 1197494--1197574 Score: 119
Period size: 39 Copynumber: 2.1 Consensus size: 39
1197484 ATTTTATTTC
* *
1197494 GGTCGGGTCGGGTCTTGGGTGGAGGATCCCTTGTTATCG
1 GGTCGGGTCGAGTCTCGGGTGGAGGATCCCTTGTTATCG
*
1197533 GGTCGGGTCGAGTCTCGGGTGGAGGA-CCTCTTGTTCTCG
1 GGTCGGGTCGAGTCTCGGGTGGAGGATCC-CTTGTTATCG
1197572 GGT
1 GGT
1197575 TTGGTCGGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 2 0.05
39 36 0.95
ACGTcount: A:0.07, C:0.20, G:0.43, T:0.30
Consensus pattern (39 bp):
GGTCGGGTCGAGTCTCGGGTGGAGGATCCCTTGTTATCG
Found at i:1210799 original size:100 final size:101
Alignment explanation
Indices: 1210647--1210844 Score: 344
Period size: 100 Copynumber: 2.0 Consensus size: 101
1210637 ATTGTTTTGA
*
1210647 TTATTTTTAGTTTGGCTTATTTTTTTTACTATTTTAAGTTCAAATTATTTTAGATTTGATTTAAT
1 TTATTTTTAGTTTGGCTTATTTTTTTTACTATTCTAAGTTCAAATTATTTTAGATTTGATTTAAT
**
1210712 TTCAAGGTTAAGTTATTTTATGTTTGAGCCATTAAG
66 TTCAAAATTAAGTTATTTTATGTTTGAGCCATTAAG
* *
1210748 TTATTTTTAGTTTGGGTTA-TTTTTTTACTATTCTAAGTTCAAGTTATTTTAGATTTGATTTAAT
1 TTATTTTTAGTTTGGCTTATTTTTTTTACTATTCTAAGTTCAAATTATTTTAGATTTGATTTAAT
1210812 TTCAAAATTAAGTTATTTTATGTTTGAGCCATT
66 TTCAAAATTAAGTTATTTTATGTTTGAGCCATT
1210845 TCGGGTTCAA
Statistics
Matches: 92, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
100 74 0.80
101 18 0.20
ACGTcount: A:0.26, C:0.06, G:0.13, T:0.56
Consensus pattern (101 bp):
TTATTTTTAGTTTGGCTTATTTTTTTTACTATTCTAAGTTCAAATTATTTTAGATTTGATTTAAT
TTCAAAATTAAGTTATTTTATGTTTGAGCCATTAAG
Found at i:1211158 original size:12 final size:12
Alignment explanation
Indices: 1211141--1211165 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1211131 ATACGTTGAC
1211141 TAATAATTTTCA
1 TAATAATTTTCA
1211153 TAATAATTTTCA
1 TAATAATTTTCA
1211165 T
1 T
1211166 CCACCAAAGA
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:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TAATAATTTTCA
Found at i:1211474 original size:14 final size:14
Alignment explanation
Indices: 1211452--1211498 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
1211442 TAAATTCATA
*
1211452 TTTAAGATTTAGGG
1 TTTATGATTTAGGG
*
1211466 TTTATGATTTAGGT
1 TTTATGATTTAGGG
*
1211480 TTTATAATTTTAGGG
1 TTTATGA-TTTAGGG
1211495 TTTA
1 TTTA
1211499 GACTTCACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 18 0.64
15 10 0.36
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.53
Consensus pattern (14 bp):
TTTATGATTTAGGG
Found at i:1211694 original size:22 final size:22
Alignment explanation
Indices: 1211645--1211694 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
1211635 AGAACTTATA
* *
1211645 ATTTAAGGGTTTAAAGTTTAGGG
1 ATTT-AGGATTTAAAGTTTAGAG
* *
1211668 TTTTAGGATTTATAGTTTAGAG
1 ATTTAGGATTTAAAGTTTAGAG
1211690 ATTTA
1 ATTTA
1211695 TTATACTTGC
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.46
Consensus pattern (22 bp):
ATTTAGGATTTAAAGTTTAGAG
Found at i:1212458 original size:21 final size:21
Alignment explanation
Indices: 1212432--1212476 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1212422 GATTTCTGGG
* *
1212432 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1212453 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1212474 CAA
1 CAA
1212477 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1213363 original size:31 final size:31
Alignment explanation
Indices: 1213325--1213478 Score: 247
Period size: 31 Copynumber: 5.0 Consensus size: 31
1213315 GGGTCGAGGG
1213325 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
1213356 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
1213387 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
* * * *
1213418 TTACCTATGTCCTTCGGGACATATGAACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGT
*
1213449 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
1213479 GTCCTTCGGG
Statistics
Matches: 114, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 113 0.99
32 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGT
Found at i:1216465 original size:21 final size:21
Alignment explanation
Indices: 1216439--1216483 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1216429 GATTTCTGGG
* *
1216439 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1216460 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1216481 CAA
1 CAA
1216484 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1217386 original size:31 final size:31
Alignment explanation
Indices: 1217348--1217501 Score: 247
Period size: 31 Copynumber: 5.0 Consensus size: 31
1217338 GGGTCGAGGG
1217348 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
1217379 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
*
1217410 TTACCTATGTTCTTCGGAATATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
* * *
1217441 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGT
*
1217472 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
1217502 GTCCTTCGGG
Statistics
Matches: 114, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 113 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGT
Found at i:1218500 original size:68 final size:68
Alignment explanation
Indices: 1218420--1218581 Score: 290
Period size: 68 Copynumber: 2.4 Consensus size: 68
1218410 GAATTTATGA
1218420 TTTATAGTTTAAGATTTTATAATTTTAAGATTCGAAGGTTTAGGATTTTAGAAGGTAGGGTTTTA
1 TTTATAGTTTAAGATTTTATAATTTTAAGATTCGAAGGTTTAGGATTTTAGAAGGTAGGGTTTTA
1218485 GGG
66 GGG
*
1218488 TTTATAGTTTAAGATTTTATAATTTTAAGATTTGAAGGTTTAGGATTTTAGAAGGTAGGGTTTTA
1 TTTATAGTTTAAGATTTTATAATTTTAAGATTCGAAGGTTTAGGATTTTAGAAGGTAGGGTTTTA
1218553 GGG
66 GGG
* *
1218556 TTTATATTTTAAGATTTGAT-ATTTTA
1 TTTATAGTTTAAGATTTTATAATTTTA
1218582 GGTTTTAGGG
Statistics
Matches: 91, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
67 6 0.07
68 85 0.93
ACGTcount: A:0.30, C:0.01, G:0.22, T:0.48
Consensus pattern (68 bp):
TTTATAGTTTAAGATTTTATAATTTTAAGATTCGAAGGTTTAGGATTTTAGAAGGTAGGGTTTTA
GGG
Found at i:1218506 original size:15 final size:16
Alignment explanation
Indices: 1218488--1218520 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1218478 GGTTTTAGGG
1218488 TTTAT-AGTTTAAGAT
1 TTTATAAGTTTAAGAT
*
1218503 TTTATAATTTTAAGAT
1 TTTATAAGTTTAAGAT
1218519 TT
1 TT
1218521 GAAGGTTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (16 bp):
TTTATAAGTTTAAGAT
Found at i:1218636 original size:14 final size:14
Alignment explanation
Indices: 1218615--1218665 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
1218605 GTTTAGAGTG
1218615 TATGGTTTAAGATT
1 TATGGTTTAAGATT
* * *
1218629 TATAGTTTAGGTTT
1 TATGGTTTAAGATT
* *
1218643 TAGGGTTTGAGATT
1 TATGGTTTAAGATT
1218657 TATGGTTTA
1 TATGGTTTA
1218666 TGTTTGATAT
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.24, C:0.00, G:0.25, T:0.51
Consensus pattern (14 bp):
TATGGTTTAAGATT
Found at i:1218636 original size:28 final size:28
Alignment explanation
Indices: 1218563--1218665 Score: 77
Period size: 28 Copynumber: 3.6 Consensus size: 28
1218553 GGGTTTATAT
* *
1218563 TTTAAGATTTGATATTTTAGGTTTTAGGG
1 TTTAAGATTT-ATAGTTTAGGTTGTAGGG
* * *
1218592 TGT-ACATTCTA-AGGTTTAGAG-TGTATGG
1 TTTAAGATT-TATA-GTTTAG-GTTGTAGGG
*
1218620 TTTAAGATTTATAGTTTAGGTTTTAGGG
1 TTTAAGATTTATAGTTTAGGTTGTAGGG
* *
1218648 TTTGAGATTTATGGTTTA
1 TTTAAGATTTATAGTTTA
1218666 TGTTTGATAT
Statistics
Matches: 57, Mismatches: 11, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
27 2 0.04
28 46 0.81
29 9 0.16
ACGTcount: A:0.24, C:0.02, G:0.25, T:0.49
Consensus pattern (28 bp):
TTTAAGATTTATAGTTTAGGTTGTAGGG
Found at i:1218974 original size:23 final size:23
Alignment explanation
Indices: 1218946--1218992 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
1218936 GGTTTAAGGA
1218946 TTAATGTTTTGAGATTGAGGATT
1 TTAATGTTTTGAGATTGAGGATT
* *
1218969 TTAATGTTTTGTGATTTAGGATT
1 TTAATGTTTTGAGATTGAGGATT
1218992 T
1 T
1218993 AGGGGTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.53
Consensus pattern (23 bp):
TTAATGTTTTGAGATTGAGGATT
Found at i:1222388 original size:18 final size:19
Alignment explanation
Indices: 1222353--1222389 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1222343 CACGGAATGT
1222353 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1222373 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
1222390 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1222569 original size:36 final size:37
Alignment explanation
Indices: 1222536--1222604 Score: 106
Period size: 35 Copynumber: 1.9 Consensus size: 37
1222526 TACAAATTGT
1222536 AAAATATTTATAT-ATTTTCTTTA-AAAATTAAATTC
1 AAAATATTTATATAATTTTCTTTACAAAATTAAATTC
* *
1222571 ATAATATTTATATAATTTTTTTTACAAAATTAAA
1 AAAATATTTATATAATTTTCTTTACAAAATTAAA
1222605 AATATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 12 0.40
36 9 0.30
37 9 0.30
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.49
Consensus pattern (37 bp):
AAAATATTTATATAATTTTCTTTACAAAATTAAATTC
Found at i:1223034 original size:34 final size:34
Alignment explanation
Indices: 1222996--1223088 Score: 150
Period size: 34 Copynumber: 2.7 Consensus size: 34
1222986 CAAAATGTTG
*
1222996 TACTTTTTAAGTGGGGTCATGATACAAAGTGTCA
1 TACTTTTCAAGTGGGGTCATGATACAAAGTGTCA
**
1223030 TACTTTTCAAGTGGGGTCATGATACAAAGTGTTT
1 TACTTTTCAAGTGGGGTCATGATACAAAGTGTCA
*
1223064 TACTTTTCAAGTGGGGTAATGATAC
1 TACTTTTCAAGTGGGGTCATGATAC
1223089 TACAATTTTA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 55 1.00
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.37
Consensus pattern (34 bp):
TACTTTTCAAGTGGGGTCATGATACAAAGTGTCA
Found at i:1224051 original size:5 final size:5
Alignment explanation
Indices: 1224041--1224073 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
1224031 TCTTCTCTCT
*
1224041 CTCCC CTCCC CTCCC CTCCC CTCCC ATCCC CTC
1 CTCCC CTCCC CTCCC CTCCC CTCCC CTCCC CTC
1224074 ATGTGATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.03, C:0.76, G:0.00, T:0.21
Consensus pattern (5 bp):
CTCCC
Found at i:1228076 original size:31 final size:31
Alignment explanation
Indices: 1228041--1228144 Score: 93
Period size: 31 Copynumber: 3.2 Consensus size: 31
1228031 CAGTCGGTGT
* *
1228041 TGAACCTATAAAAGAAATTACAAGCAGCGAC
1 TGAACCTATAAAAGAAATTACCAGCAGTGAC
* * *
1228072 TGAACTTGCCAGAGATAGAAATTACCAGTCAGTG-C
1 TGAAC---CTATA-AAAGAAATTACCAG-CAGTGAC
* *
1228107 TGAACCTATACAAGGAATTACCAGCAGTGAC
1 TGAACCTATAAAAGAAATTACCAGCAGTGAC
1228138 TGAACCT
1 TGAACCT
1228145 GGCAGAGTCT
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
30 5 0.09
31 24 0.42
32 3 0.05
34 3 0.05
35 18 0.32
36 4 0.07
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.20
Consensus pattern (31 bp):
TGAACCTATAAAAGAAATTACCAGCAGTGAC
Found at i:1229226 original size:27 final size:27
Alignment explanation
Indices: 1229186--1229259 Score: 130
Period size: 27 Copynumber: 2.7 Consensus size: 27
1229176 AGATACTTTA
1229186 GTCATTTTACACTTTAAGGGCATTTTG
1 GTCATTTTACACTTTAAGGGCATTTTG
*
1229213 GTCATTTTATACTTTAAGGGCATTTTG
1 GTCATTTTACACTTTAAGGGCATTTTG
*
1229240 GTCATTTTACACTTCAAGGG
1 GTCATTTTACACTTTAAGGG
1229260 AAATTTCGTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (27 bp):
GTCATTTTACACTTTAAGGGCATTTTG
Found at i:1230284 original size:22 final size:22
Alignment explanation
Indices: 1230252--1230316 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
1230242 CAAGGTTAAA
*
1230252 GTCAACGTCAACG-GTTAGACTG
1 GTCAAAGTCAACGAGTT-GACTG
*
1230274 GTTAAAGTCAACGAGTTGACTG
1 GTCAAAGTCAACGAGTTGACTG
*
1230296 GTCAATGTCAACGAGTTGACT
1 GTCAAAGTCAACGAGTTGACT
1230317 CAGCAACTAG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
22 35 0.92
23 3 0.08
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.26
Consensus pattern (22 bp):
GTCAAAGTCAACGAGTTGACTG
Found at i:1231682 original size:21 final size:21
Alignment explanation
Indices: 1231656--1231698 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1231646 CCTAGAATGG
*
1231656 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
1231677 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
1231698 A
1 A
1231699 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:1231826 original size:21 final size:21
Alignment explanation
Indices: 1231800--1231892 Score: 74
Period size: 21 Copynumber: 4.7 Consensus size: 21
1231790 TCTCGGAGCC
1231800 GGGAATCTGTACCCCCTGGGG
1 GGGAATCTGTACCCCCTGGGG
*
1231821 GGGAATCTGT--TCCC----G
1 GGGAATCTGTACCCCCTGGGG
*
1231836 GGGAATC-GATACCCCCTGAGG
1 GGGAATCTG-TACCCCCTGGGG
* * **
1231857 GGGAATATGTTCATCCTGGGG
1 GGGAATCTGTACCCCCTGGGG
1231878 GGGAATCTGTACCCC
1 GGGAATCTGTACCCC
1231893 TGGACAATCT
Statistics
Matches: 53, Mismatches: 11, Indels: 16
0.66 0.14 0.20
Matches are distributed among these distances:
14 1 0.02
15 9 0.17
17 3 0.06
19 3 0.06
21 36 0.68
22 1 0.02
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.22
Consensus pattern (21 bp):
GGGAATCTGTACCCCCTGGGG
Found at i:1231849 original size:36 final size:36
Alignment explanation
Indices: 1231800--1231868 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
1231790 TCTCGGAGCC
* *
1231800 GGGAATCTGTACCCCCTGGGGGGGAATCTGTTCCCG
1 GGGAATCTGTACCCCCTGAGGGGGAATATGTTCCCG
1231836 GGGAATC-GATACCCCCTGAGGGGGAATATGTTC
1 GGGAATCTG-TACCCCCTGAGGGGGAATATGTTC
1231869 ATCCTGGGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 1 0.03
36 29 0.97
ACGTcount: A:0.19, C:0.25, G:0.35, T:0.22
Consensus pattern (36 bp):
GGGAATCTGTACCCCCTGAGGGGGAATATGTTCCCG
Found at i:1238807 original size:63 final size:63
Alignment explanation
Indices: 1238689--1238807 Score: 159
Period size: 63 Copynumber: 1.9 Consensus size: 63
1238679 CTAGTAAAAT
* * *
1238689 GACTTCGAAAGGTGTTGATCGACTGCATGGCGAAACTAAAAGTAACGGATTTGATTGTAAACA
1 GACTTCAAAAGGTGTTGATCAACTGCATGGCGAAACTAAAAGTAACGGATCTGATTGTAAACA
* * * *
1238752 GACTTCAAAATGTGTTGATCAATTGCATGGC-AGAACTAAAAGTAATGGGTCTGATT
1 GACTTCAAAAGGTGTTGATCAACTGCATGGCGA-AACTAAAAGTAACGGATCTGATT
1238808 ATAATGATGT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
62 1 0.02
63 47 0.98
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.28
Consensus pattern (63 bp):
GACTTCAAAAGGTGTTGATCAACTGCATGGCGAAACTAAAAGTAACGGATCTGATTGTAAACA
Found at i:1241192 original size:183 final size:183
Alignment explanation
Indices: 1240854--1241210 Score: 435
Period size: 183 Copynumber: 2.0 Consensus size: 183
1240844 CACTCTGATG
* * * *
1240854 AGGTAAGATTTGTTGATTCCCAGTTACATTGCAATTTTGGCGAGAAACATGAAGCAACAGAAATA
1 AGGTAAGATTGGTTGATGCACAGTTACATTGCAAGTTTGGCGAGAAACATGAAGCAACAGAAATA
* * *** * * * * *
1240919 GCTCGTGAGATGGAAGCAGACTGTAGTACAGAATATAAAGAGGAGAATTGTCCTGAAACTCTTAT
66 GCACATGAGATGGAAGCAGACCAAAGTACAGAATACAAACACGAGAATTGTCCTGAAACCCTGAT
*
1240984 GAAGAAAGAGAGGGAAACAAAAAATGCTTGCCGAGAAGAAGTTACATTGAAGC
131 GAAGAAAGAGAGGGAAACAAAAAATGCTTCCCGAGAAGAAGTTACATTGAAGC
* * * ** * *
1241037 AGGTAAGATTGGTTGATGCACAGTTACATTGCGAGTTTGGGGAGAAACATGAATCTGCGGAAATG
1 AGGTAAGATTGGTTGATGCACAGTTACATTGCAAGTTTGGCGAGAAACATGAAGCAACAGAAATA
* * * *
1241102 GCACATGAGATTGAAGCAGGCCAAAGTTCAGAATGCAAACACGAGAATTGTCCTGAAACCCTGAT
66 GCACATGAGATGGAAGCAGACCAAAGTACAGAATACAAACACGAGAATTGTCCTGAAACCCTGAT
** * * *
1241167 GAAGGTAGAGAGTGAAACCAAAAATGCTTCCCGGGAAGAAGTTA
131 GAAGAAAGAGAGGGAAACAAAAAATGCTTCCCGAGAAGAAGTTA
1241211 AGCTAGTGAA
Statistics
Matches: 143, Mismatches: 31, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
183 143 1.00
ACGTcount: A:0.38, C:0.14, G:0.27, T:0.22
Consensus pattern (183 bp):
AGGTAAGATTGGTTGATGCACAGTTACATTGCAAGTTTGGCGAGAAACATGAAGCAACAGAAATA
GCACATGAGATGGAAGCAGACCAAAGTACAGAATACAAACACGAGAATTGTCCTGAAACCCTGAT
GAAGAAAGAGAGGGAAACAAAAAATGCTTCCCGAGAAGAAGTTACATTGAAGC
Found at i:1247914 original size:16 final size:17
Alignment explanation
Indices: 1247884--1247915 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1247874 GTATCGCCGA
1247884 CAAAATTTCACTATTCC
1 CAAAATTTCACTATTCC
1247901 CAAAATTT-ACTATTC
1 CAAAATTTCACTATTC
1247916 ACGTGAACAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.38, C:0.25, G:0.00, T:0.38
Consensus pattern (17 bp):
CAAAATTTCACTATTCC
Found at i:1254454 original size:3 final size:3
Alignment explanation
Indices: 1254448--1254531 Score: 96
Period size: 3 Copynumber: 27.7 Consensus size: 3
1254438 TTTCATATAG
* ** *
1254448 TTA TTA TTA TTA TTA TTA TGA TTA TTA AAA TTA TTA TTT TTA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* * *
1254497 TTA TTA TTA ATA TTA TTA CTA TTA ATA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1254532 TTAAAAAATA
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
3 63 0.95
4 3 0.05
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:1256062 original size:21 final size:21
Alignment explanation
Indices: 1256036--1256078 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1256026 TTTTAAATAA
1256036 AAATAAATAT-TTTACTTTTAT
1 AAATAAATATATTT-CTTTTAT
*
1256057 AAATAAATCTATTTCTTTTAT
1 AAATAAATATATTTCTTTTAT
1256078 A
1 A
1256079 TATATTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATAAATATATTTCTTTTAT
Found at i:1258509 original size:18 final size:18
Alignment explanation
Indices: 1258486--1258531 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1258476 TCATAACCCG
1258486 ACCCGAACC-GACCCGTTT
1 ACCCG-ACCTGACCCGTTT
*
1258504 ACCCGACCTGACCCGTTG
1 ACCCGACCTGACCCGTTT
*
1258522 ACACGACCTG
1 ACCCGACCTG
1258532 TTGACCATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 3 0.12
18 22 0.88
ACGTcount: A:0.22, C:0.43, G:0.20, T:0.15
Consensus pattern (18 bp):
ACCCGACCTGACCCGTTT
Found at i:1262925 original size:21 final size:21
Alignment explanation
Indices: 1262900--1262942 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1262890 GAATTAAAAA
1262900 TAATGACCAAGAATAAAACAT
1 TAATGACCAAGAATAAAACAT
1262921 TAATGACCAAGAATAAAACAT
1 TAATGACCAAGAATAAAACAT
1262942 T
1 T
1262943 GAAGAAATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.56, C:0.14, G:0.09, T:0.21
Consensus pattern (21 bp):
TAATGACCAAGAATAAAACAT
Found at i:1265855 original size:1 final size:1
Alignment explanation
Indices: 1265845--1266029 Score: 136
Period size: 1 Copynumber: 185.0 Consensus size: 1
1265835 ATATACTCAT
* * * * * * * *
1265845 AAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * * * *
1265910 AGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * ** * *
1265975 AAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAGGAAAAAAGAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1266030 TTGAATCAAG
Statistics
Matches: 134, Mismatches: 50, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 134 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (1 bp):
A
Found at i:1265857 original size:7 final size:7
Alignment explanation
Indices: 1265845--1266029 Score: 338
Period size: 7 Copynumber: 26.6 Consensus size: 7
1265835 ATATACTCAT
1265845 AAAAAGA
1 AAAAAGA
1265852 AAAAAGA
1 AAAAAGA
1265859 AAAAAGA
1 AAAAAGA
1265866 AAAAAGA
1 AAAAAGA
1265873 AAAAAGA
1 AAAAAGA
1265880 AAAAAGA
1 AAAAAGA
1265887 AAAAAGA
1 AAAAAGA
1265894 AAAAA-A
1 AAAAAGA
1265900 AAAAAG-
1 AAAAAGA
1265906 AAAAAGA
1 AAAAAGA
1265913 AAAAAGA
1 AAAAAGA
1265920 AAAAAGA
1 AAAAAGA
1265927 AAAAAGA
1 AAAAAGA
1265934 AAAAAGA
1 AAAAAGA
1265941 AAAAAGA
1 AAAAAGA
1265948 AAAAAGA
1 AAAAAGA
1265955 AAAAAGA
1 AAAAAGA
1265962 AAAAAGA
1 AAAAAGA
1265969 AAAAAGA
1 AAAAAGA
1265976 AAAAAGA
1 AAAAAGA
1265983 AAAAAGA
1 AAAAAGA
1265990 AAAAAGA
1 AAAAAGA
1265997 AAAAAGA
1 AAAAAGA
*
1266004 AAAAGGA
1 AAAAAGA
1266011 AAAAAGAA
1 AAAAAG-A
1266019 AAAAAGA
1 AAAAAGA
1266026 AAAA
1 AAAA
1266030 TTGAATCAAG
Statistics
Matches: 173, Mismatches: 2, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
6 12 0.07
7 154 0.89
8 7 0.04
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:1270733 original size:44 final size:44
Alignment explanation
Indices: 1270670--1270756 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 44
1270660 TACATCTACA
1270670 CTCTTCAAAGATGATAGATTCTCTCTTCAAAGAT-AATAGATTTT
1 CTCTTCAAAGATGATAGATTCTCTCTTCAAAGATGAAT-GATTTT
*
1270714 CTCTTCAAAGATGATAGATTCTCTTTTCAAAGATGAATGATTT
1 CTCTTCAAAGATGATAGATTCTCTCTTCAAAGATGAATGATTT
1270757 ATTGGATTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
44 38 0.93
45 3 0.07
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (44 bp):
CTCTTCAAAGATGATAGATTCTCTCTTCAAAGATGAATGATTTT
Found at i:1270755 original size:22 final size:22
Alignment explanation
Indices: 1270670--1270749 Score: 133
Period size: 22 Copynumber: 3.6 Consensus size: 22
1270660 TACATCTACA
1270670 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
* *
1270692 CTCTTCAAAGATAATAGATTTT
1 CTCTTCAAAGATGATAGATTCT
1270714 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
1270736 CTTTTCAAAGATGA
1 CTCTTCAAAGATGA
1270750 ATGATTTATT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCT
Done.