Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008654.1 Hibiscus syriacus cultivar Beakdansim tig00111648_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: 3533819
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 18
Found at i:1093766 original size:18 final size:17
Alignment explanation
Indices: 1093712--1093760 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
1093702 TTGGACTCTC
* *
1093712 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
1093730 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
1093748 AGTGCATTCGATG
1 AGTGCA-TCGATG
1093761 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:1093930 original size:65 final size:66
Alignment explanation
Indices: 1093732--1093941 Score: 227
Period size: 65 Copynumber: 3.2 Consensus size: 66
1093722 TGCACTAAGA
* * * *
1093732 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAAT-AGCCA-GAGTGCATCGATGCAT-GAC
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATCCATG-GTGCATCGATGCATGGAT
1093794 TG
65 TG
* * * * *
1093796 GTGCATCGATGCATCAAATGCATTCAATGTTTTC-ATAAAATCCTTAGTGCATCGGTGCATGG-T
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAATATAATCCATGGTGCATCGATGCATGGAT
1093859 AT-
65 -TG
* * *
1093861 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATCCATGGTGCATCGATGCATGGATT
1093925 G
66 G
*
1093926 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
1093942 CTCTGAAAAT
Statistics
Matches: 119, Mismatches: 19, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
63 3 0.03
64 52 0.44
65 62 0.52
66 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.31
Consensus pattern (66 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATCCATGGTGCATCGATGCATGGATT
G
Found at i:1094674 original size:19 final size:20
Alignment explanation
Indices: 1094636--1094675 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1094626 AGTATCAGTG
1094636 TCATTATATAACCTACAATA
1 TCATTATATAACCTACAATA
* *
1094656 TCATTTTAT-ACCTATAATA
1 TCATTATATAACCTACAATA
1094675 T
1 T
1094676 TATATAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.42
Consensus pattern (20 bp):
TCATTATATAACCTACAATA
Found at i:1095025 original size:226 final size:226
Alignment explanation
Indices: 1094591--1095045 Score: 607
Period size: 226 Copynumber: 2.0 Consensus size: 226
1094581 AGTAAATTGA
** * *
1094591 TTTCCTTCAAAGGAATGGGAATACTCTCTACTACAAGTATCAGTGTCATTATATAACCTACAATA
1 TTTCCTTCAAAGGAATGGGAATACTCTCTACTACAAGTATCAGTACCATTATATAACCAAAAATA
* ** *
1094656 TCATTTTATACCTATAATATTATATAAAAGTATTGATATTTATTTTCTACCTAAAATATCACTTT
66 ACATTTTATACCTATAATATTATATAAAAGTATCAATATTAATTTTCTACCTAAAATATCACTTT
* *
1094721 CAAACTGTAATAAGTTCCAAATCCTTCTTTACTTCAAAAACCCAAACCCATAAACCTAGTCCTAT
131 CAAACTATAATAAGTTCCAAATCCTTCTTTACTTCAAAAACCCAAACCCATAAACCTAGACCTAT
* *
1094786 TTCTGAATATTGTAATACTAAAAAACTAGGG
196 TTCTCAATATTGTAATACTAAAAAACTAAGG
* *
1094817 TTTCCTTCAAAGG-ATGGGCATACTCTCTACTACAAGTATC-GATACCTTATATATAACCAAAAA
1 TTTCCTTCAAAGGAATGGGAATACTCTCTACTACAAGTATCAG-TACCAT-TATATAACCAAAAA
* *
1094880 TAACATTTTCTACCTATAATATTATATAAAAGTATCAATATTAATTTTCTACCTAGAATATCACT
64 TAACATTTTATACCTATAATATTATATAAAAGTATCAATATTAATTTTCTACCTAAAATATCACT
* * * * *
1094945 TTC-TACTATAAT-CGTTCTCAAATGCTT-TTTGCTTCAAAAACCCCAAACCCATAAACTTA-AC
129 TTCAAACTATAATAAGTTC-CAAATCCTTCTTTACTTCAAAAA-CCCAAACCCATAAACCTAGAC
* *
1095006 CTATATTTTCAATTATTGTAATACTAAAACACTAAGG
192 CTAT-TTCTCAA-TATTGTAATACTAAAAAACTAAGG
1095043 TTT
1 TTT
1095046 TGACAACGTA
Statistics
Matches: 200, Mismatches: 23, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
224 22 0.11
225 66 0.33
226 112 0.56
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.36
Consensus pattern (226 bp):
TTTCCTTCAAAGGAATGGGAATACTCTCTACTACAAGTATCAGTACCATTATATAACCAAAAATA
ACATTTTATACCTATAATATTATATAAAAGTATCAATATTAATTTTCTACCTAAAATATCACTTT
CAAACTATAATAAGTTCCAAATCCTTCTTTACTTCAAAAACCCAAACCCATAAACCTAGACCTAT
TTCTCAATATTGTAATACTAAAAAACTAAGG
Found at i:1095732 original size:198 final size:198
Alignment explanation
Indices: 1095260--1095809 Score: 560
Period size: 198 Copynumber: 2.8 Consensus size: 198
1095250 TACGTTTGTG
* * * * *
1095260 TAAGGTATCGATACTTTCGATACATTTTTATTTTTTCATTTGTTTTTAATTCCTAAAGTATTGAT
1 TAAGGTATCGATAATTTCGAGACA-TTTTATTTTTTCATTTCTTTTAAATTCCTAAAGTATCGAT
* * ** * * * * *
1095325 TCTATGACACATATACTTATAAAAGTATCAATAC--CTTT-AA-CATATCCAATAGCACTTTACC
65 ACTTTGGTACATATACTTATAAAAGTATCGATACAAATTTCAACCAT-TCCGATAACTCTTTACC
* * * * * * **
1095386 AGTTTTTCATATTGAAACCGGATTTATTAAATTTTAACCTATTATATTGTCATGTATTGATACAT
129 AGTTTTTCAAATTGAAATCGGTTTTGTCAAACTTTAACCTATTATATTGTCATGTATCAATACAT
*
1095451 GTGTC
194 GTGTA
* * * ** * * *
1095456 TAAGGT-TCGAT-ACTTCATAGGC--GCTATTATTACATTTCTTTTAAATTCCTAAAGTACCGAT
1 TAAGGTATCGATAATTTC-GAGACATTTTATTTTTTCATTTCTTTTAAATTCCTAAAGTATCGAT
* * *
1095517 ACTTTGGTGCATATACTTATAAAAGTATCGATACAAATTTCAACCATTCCGATATCTCTTTACCG
65 ACTTTGGTACATATACTTATAAAAGTATCGATACAAATTTCAACCATTCCGATAACTCTTTACCA
* *
1095582 GTTTTGTCAAACTGAAATCGGTTTTGTCAAACTTTAACCTGTTATATTGTCATGTATCAATACAT
130 GTTTT-TCAAATTGAAATCGGTTTTGTCAAACTTTAACCTATTATATTGTCATGTATCAATACAT
1095647 GTGTA
194 GTGTA
* * *
1095652 TAAGGTATCAATAATTTCGAGACATTTTCTTTTTTCATTT-TTTTAAATTCCTACAGTATCGATA
1 TAAGGTATCGATAATTTCGAGACATTTTATTTTTTCATTTCTTTTAAATTCCTAAAGTATCGATA
* * * * * *
1095716 CTTTGGTACATATACTTATACACGTATCGATACAAATTTCAACAATTCTGGTAACTCTTTACTAG
66 CTTTGGTACATATACTTATAAAAGTATCGATACAAATTTCAACCATTCCGATAACTCTTTACCAG
** *
1095781 TTTTCTCAAATTTTAATTGGTTTTGTCAA
131 TTTT-TCAAATTGAAATCGGTTTTGTCAA
1095810 TTTCCAATCG
Statistics
Matches: 284, Mismatches: 60, Indels: 18
0.78 0.17 0.05
Matches are distributed among these distances:
192 59 0.21
194 6 0.02
195 28 0.10
196 68 0.24
197 7 0.02
198 106 0.37
199 10 0.04
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (198 bp):
TAAGGTATCGATAATTTCGAGACATTTTATTTTTTCATTTCTTTTAAATTCCTAAAGTATCGATA
CTTTGGTACATATACTTATAAAAGTATCGATACAAATTTCAACCATTCCGATAACTCTTTACCAG
TTTTTCAAATTGAAATCGGTTTTGTCAAACTTTAACCTATTATATTGTCATGTATCAATACATGT
GTA
Found at i:1101850 original size:61 final size:61
Alignment explanation
Indices: 1101762--1101876 Score: 187
Period size: 61 Copynumber: 1.9 Consensus size: 61
1101752 GAAGGTGGAT
*
1101762 ACGACCTTATGTATCATGTCCGGATTAGCACTATAGCGTAAGCTTAGTGTAGGTGGTGGGC
1 ACGACCTTATGTATCATGTCCGGATTAGCACTATAGCGTAAGCTTAGTGCAGGTGGTGGGC
* *
1101823 ACGACCTTATGTGT-ATTGTCCGGATTAGCACTATGGCGTAAGCTTAGTGCAGGT
1 ACGACCTTATGTATCA-TGTCCGGATTAGCACTATAGCGTAAGCTTAGTGCAGGT
1101877 TTAGCACTAC
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
60 1 0.02
61 49 0.98
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (61 bp):
ACGACCTTATGTATCATGTCCGGATTAGCACTATAGCGTAAGCTTAGTGCAGGTGGTGGGC
Found at i:1102078 original size:46 final size:45
Alignment explanation
Indices: 1101986--1102154 Score: 250
Period size: 45 Copynumber: 3.8 Consensus size: 45
1101976 GTAACCATGC
*
1101986 AAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1102030 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAA-TAAATGGTAAGTATATTGGTA
** * * *
1102076 AAATAAGCTTACGAGCTTATAAAACAAATGGTAAGTATGTTGATA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
1102121 AAATAAGCTTACGAGCTTATGGGAGAAATGGTAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAA
1102155 AATATTGAAA
Statistics
Matches: 113, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
44 24 0.21
45 49 0.43
46 40 0.35
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.29
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:1106064 original size:139 final size:139
Alignment explanation
Indices: 1105702--1106218 Score: 691
Period size: 139 Copynumber: 3.7 Consensus size: 139
1105692 CTTTTGTGAT
* * * **
1105702 TGAAACGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCACTCATCAAATGAGTT
1 TGAATCGAGTTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTT
* *
1105767 CTTCTCGTTATGAACTCTCCACTGGAAATGTTGATCCCTTGAGTGAGG-TGTTGCTGATTCAACT
66 CTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGAT-TTGCTGATTCAACT
1105831 CCATATATGA
130 CCATATATGA
* * * * *
1105841 TAAATTGAGCTAAAGGTTGAACAAGTTATTCTCAGTATGAACTTCTTCTCCCTCATCGGATGAGT
1 TGAATCGAG-TTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGT
*
1105906 TCTTCTCATTATGAACTCTCTACTGGAAATGTTGATCCCTCGAGTGAGGATTTGCTGATTCAACT
65 TCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGATTTGCTGATTCAACT
*
1105971 CCTTATATGA
130 CCATATATGA
* *
1105981 TGAATCGAGTTAAGGTTGAACAAGTTCTTTTCATTATGAACTTCTTCTCCCTCATCGGGTGAGTT
1 TGAATCGAGTTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTT
* ** * * *
1106046 ATTCTCATTATGAACTCTCCACTACAAATGTTTATCCCTCGAGTGAGGCA-TTGTTGGTTCAACT
66 CTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGG-ATTTGCTGATTCAACT
*
1106110 CCATATGTGA
130 CCATATATGA
** *
1106120 TGAATCGA--TAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCAAATGAGTG
1 TGAATCGAGTTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTT
* * * * *
1106183 CTTCTTATTACGAACCTTTCCAATGGAAATATTGAT
66 CTTCTCATTATGAA-CTCTCCACTGGAAATGTTGAT
1106219 TGGTTTATCC
Statistics
Matches: 330, Mismatches: 44, Indels: 9
0.86 0.11 0.02
Matches are distributed among these distances:
137 61 0.18
138 15 0.05
139 128 0.39
140 125 0.38
141 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (139 bp):
TGAATCGAGTTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTT
CTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGATTTGCTGATTCAACTC
CATATATGA
Found at i:1109356 original size:4 final size:4
Alignment explanation
Indices: 1109347--1109389 Score: 58
Period size: 4 Copynumber: 11.8 Consensus size: 4
1109337 CTTGATCAAT
1109347 TTTC TTTC -TT- TTTC TTTC TTTC TTTC TTTC TTT- TTTC -TTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
1109390 TTATTTTTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
3 10 0.29
4 25 0.71
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTC
Found at i:1109370 original size:18 final size:17
Alignment explanation
Indices: 1109346--1109472 Score: 74
Period size: 18 Copynumber: 7.8 Consensus size: 17
1109336 ACTTGATCAA
1109346 TTTTCTTTCTTTTTCTT
1 TTTTCTTTCTTTTTCTT
1109363 TCTTTCTTTC--TTTCTT
1 T-TTTCTTTCTTTTTCTT
*
1109379 TTTTC-TTCTTTTT-AT
1 TTTTCTTTCTTTTTCTT
* **
1109394 TTTTC-CTCTTTTTCCC
1 TTTTCTTTCTTTTTCTT
*
1109410 TCTT-TTTC--TTTCTT
1 TTTTCTTTCTTTTTCTT
* *
1109424 TTCTCTCTCTTTTCTCTT
1 TTTTCTTTCTTTT-TCTT
* * *
1109442 TTTTATCTCTTTTTATGT
1 TTTTCTTTCTTTTTCT-T
1109460 TTTTC-TTCTTTTT
1 TTTTCTTTCTTTTT
1109473 GTTATATTTT
Statistics
Matches: 84, Mismatches: 16, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
14 9 0.11
15 20 0.24
16 15 0.18
17 12 0.14
18 28 0.33
ACGTcount: A:0.02, C:0.22, G:0.01, T:0.75
Consensus pattern (17 bp):
TTTTCTTTCTTTTTCTT
Found at i:1109375 original size:22 final size:22
Alignment explanation
Indices: 1109347--1109389 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1109337 CTTGATCAAT
1109347 TTTCTTTC-TTTTTCTTTCTTTC
1 TTTCTTTCTTTTTTC-TTCTTTC
1109369 TTTCTTTCTTTTTTCTTCTTT
1 TTTCTTTCTTTTTTCTTCTTT
1109390 TTATTTTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTCTTTCTTTTTTCTTCTTTC
Found at i:1109396 original size:14 final size:14
Alignment explanation
Indices: 1109346--1109406 Score: 52
Period size: 15 Copynumber: 4.2 Consensus size: 14
1109336 ACTTGATCAA
*
1109346 TTTTCTTTCTT-TT
1 TTTTTTTTCTTCTT
*
1109359 TCTTTCTTTCTTTCTT
1 T-TTTTTTTC-TTCTT
*
1109375 TCTTTTTTCTTCTT
1 TTTTTTTTCTTCTT
*
1109389 TTTATTTTTCCTCTT
1 TTT-TTTTTCTTCTT
1109404 TTT
1 TTT
1109407 CCCTCTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
13 1 0.03
14 15 0.38
15 21 0.52
16 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTTTTCTTCTT
Found at i:1109445 original size:9 final size:9
Alignment explanation
Indices: 1109346--1109455 Score: 52
Period size: 8 Copynumber: 12.3 Consensus size: 9
1109336 ACTTGATCAA
1109346 TTTTCT-TT
1 TTTTCTCTT
1109354 CTTTT-TCTT
1 -TTTTCTCTT
*
1109363 TCTT-TCTT
1 TTTTCTCTT
*
1109371 TCTT-TCTT
1 TTTTCTCTT
*
1109379 TTTTCT-TC
1 TTTTCTCTT
*
1109387 TTTT-TATT
1 TTTTCTCTT
*
1109395 TTTCCTCTT
1 TTTTCTCTT
*
1109404 TTTCCCTCTT
1 TTT-TCTCTT
*
1109414 TTTCTTTCTT
1 TTT-TCTCTT
* *
1109424 TTCTCTCTC
1 TTTTCTCTT
1109433 TTTTCTCTTT
1 TTTTCTC-TT
1109443 TTTATCTCTT
1 TTT-TCTCTT
1109453 TTT
1 TTT
1109456 ATGTTTTTCT
Statistics
Matches: 81, Mismatches: 13, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
7 1 0.01
8 28 0.35
9 23 0.28
10 25 0.31
11 4 0.05
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTCTCTT
Found at i:1109445 original size:20 final size:18
Alignment explanation
Indices: 1109346--1109472 Score: 78
Period size: 19 Copynumber: 6.8 Consensus size: 18
1109336 ACTTGATCAA
*
1109346 TTTTCTTTCTTTTTCTTT
1 TTTTCTCTCTTTTTCTTT
* *
1109364 CTTTCTTTCTTTCTT-TTT
1 TTTTCTCTCTTT-TTCTTT
* * * *
1109382 TCTTCTTTTTATTTTTCCTCT
1 T-TT-TCTCTCTTTTT-CTTT
*
1109403 TTTTCCCTCTTTTTCTTT
1 TTTTCTCTCTTTTTCTTT
1109421 CTTTTCTCTCTCTTTTCTCTT
1 -TTTTCTCTCT-TTTTCT-TT
* * *
1109442 TTTTATCTCTTTTTATGT
1 TTTTCTCTCTTTTTCTTT
1109460 TTTTCT-TCTTTTT
1 TTTTCTCTCTTTTT
1109473 GTTATATTTT
Statistics
Matches: 86, Mismatches: 15, Indels: 17
0.73 0.13 0.14
Matches are distributed among these distances:
17 7 0.08
18 23 0.27
19 27 0.31
20 24 0.28
21 5 0.06
ACGTcount: A:0.02, C:0.22, G:0.01, T:0.75
Consensus pattern (18 bp):
TTTTCTCTCTTTTTCTTT
Found at i:1109457 original size:10 final size:10
Alignment explanation
Indices: 1109346--1109455 Score: 72
Period size: 10 Copynumber: 11.4 Consensus size: 10
1109336 ACTTGATCAA
*
1109346 TTTTCTTTCT
1 TTTTCTCTCT
*
1109356 TTTTCTTTCTT
1 TTTTCTCTC-T
*
1109367 TCTTTCTTTCT
1 T-TTTCTCTCT
1109378 TTTT-TCT-T
1 TTTTCTCTCT
* *
1109386 CTTT-T-TAT
1 TTTTCTCTCT
1109394 TTTTC-CTCT
1 TTTTCTCTCT
*
1109403 TTTTCCCTCT
1 TTTTCTCTCT
*
1109413 TTTTCTTTC-
1 TTTTCTCTCT
1109422 TTTTCTCTCT
1 TTTTCTCTCT
1109432 CTTTTCTCT-T
1 -TTTTCTCTCT
*
1109442 TTTTATCTCT
1 TTTTCTCTCT
1109452 TTTT
1 TTTT
1109456 ATGTTTTTCT
Statistics
Matches: 83, Mismatches: 8, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
7 1 0.01
8 9 0.11
9 24 0.29
10 29 0.35
11 12 0.14
12 8 0.10
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTCTCTCT
Found at i:1109471 original size:9 final size:9
Alignment explanation
Indices: 1109346--1109472 Score: 59
Period size: 9 Copynumber: 13.4 Consensus size: 9
1109336 ACTTGATCAA
1109346 TTTTCTTTCT
1 TTTTC-TTCT
1109356 TTTTCTTTCTT
1 TTTTC-TTC-T
1109367 TCTTTCTT-T
1 T-TTTCTTCT
1109376 CTTTT-TTCT
1 -TTTTCTTCT
*
1109385 TCTTT-TTAT
1 T-TTTCTTCT
*
1109394 TTTTCCTCT
1 TTTTCTTCT
*
1109403 TTTTCCCTCT
1 TTTT-CTTCT
1109413 TTTTCTTTCT
1 TTTTC-TTCT
1109423 TTTCTCTCTCT
1 TTT-TCT-TCT
1109434 TTTCTCTT-T
1 TTT-TCTTCT
1109443 TTTATC-TCT
1 TTT-TCTTCT
* *
1109452 TTTT-ATGT
1 TTTTCTTCT
1109460 TTTTCTTCT
1 TTTTCTTCT
1109469 TTTT
1 TTTT
1109473 GTTATATTTT
Statistics
Matches: 96, Mismatches: 8, Indels: 27
0.73 0.06 0.21
Matches are distributed among these distances:
8 14 0.15
9 35 0.36
10 27 0.28
11 16 0.17
12 4 0.04
ACGTcount: A:0.02, C:0.22, G:0.01, T:0.75
Consensus pattern (9 bp):
TTTTCTTCT
Found at i:1109472 original size:10 final size:11
Alignment explanation
Indices: 1109346--1109442 Score: 83
Period size: 10 Copynumber: 8.7 Consensus size: 11
1109336 ACTTGATCAA
1109346 TTTTCTTTC-T
1 TTTTCTTTCTT
1109356 TTTTCTTTCTT
1 TTTTCTTTCTT
1109367 TCTTTCTTTCTT
1 T-TTTCTTTCTT
1109379 TTTTC-TTCTT
1 TTTTCTTTCTT
*
1109389 TTTATTTTTCCTCT
1 TTT-TCTTT-CT-T
**
1109403 TTTTCCCTC-T
1 TTTTCTTTCTT
1109413 TTTTCTTTCTT
1 TTTTCTTTCTT
* *
1109424 TTCTCTCTCTT
1 TTTTCTTTCTT
*
1109435 TTCTCTTT
1 TTTTCTTT
1109443 TTTATCTCTT
Statistics
Matches: 71, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
10 25 0.35
11 24 0.34
12 14 0.20
13 4 0.06
14 4 0.06
ACGTcount: A:0.01, C:0.25, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTCTTTCTT
Found at i:1112966 original size:33 final size:33
Alignment explanation
Indices: 1112914--1112990 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 33
1112904 TGGGCTTTTA
* *
1112914 GTTCATTTGTAATCATATTTCATATTTCAGAAC
1 GTTCCTTTATAATCATATTTCATATTTCAGAAC
* *
1112947 GTTCCTTTATAATCGTATTTCATATTTCAGAAT
1 GTTCCTTTATAATCATATTTCATATTTCAGAAC
1112980 GTTCCTTTATA
1 GTTCCTTTATA
1112991 TTTTAAGAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.48
Consensus pattern (33 bp):
GTTCCTTTATAATCATATTTCATATTTCAGAAC
Found at i:1123807 original size:26 final size:26
Alignment explanation
Indices: 1123776--1123828 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1123766 AGGGCTAAAT
1123776 TAAAAGGATACAAATGTTAAAGGCAA
1 TAAAAGGATACAAATGTTAAAGGCAA
1123802 TAAAAGGATACAAATGTTAAAGGCAA
1 TAAAAGGATACAAATGTTAAAGGCAA
1123828 T
1 T
1123829 TAAACTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.53, C:0.08, G:0.19, T:0.21
Consensus pattern (26 bp):
TAAAAGGATACAAATGTTAAAGGCAA
Found at i:1123873 original size:16 final size:16
Alignment explanation
Indices: 1123847--1123890 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
1123837 ATAAAAGGAC
*
1123847 TAAAATTAAAGGTAAAA
1 TAAAA-TAAAGATAAAA
1123864 -AAAATGAAAGATAAAA
1 TAAAAT-AAAGATAAAA
1123880 TAAAATAAAGA
1 TAAAATAAAGA
1123891 AAATAGTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 1 0.04
16 18 0.75
17 5 0.21
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.18
Consensus pattern (16 bp):
TAAAATAAAGATAAAA
Found at i:1123918 original size:14 final size:14
Alignment explanation
Indices: 1123899--1123933 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1123889 GAAAATAGTC
*
1123899 AATTAAAGTAATGA
1 AATTAAAGGAATGA
*
1123913 AATTAAAGGAGTGA
1 AATTAAAGGAATGA
1123927 AATTAAA
1 AATTAAA
1123934 TAAATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.17, T:0.26
Consensus pattern (14 bp):
AATTAAAGGAATGA
Found at i:1124390 original size:26 final size:26
Alignment explanation
Indices: 1124350--1124404 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
1124340 AGATCGAATC
*
1124350 AAACATTAACAAAAA-ATCAATTAAAT
1 AAACATTAACAAAAATA-CAATAAAAT
* *
1124376 AAACATTAGCTAAAATACAATAAAAT
1 AAACATTAACAAAAATACAATAAAAT
1124402 AAA
1 AAA
1124405 GAATCAGTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.65, C:0.11, G:0.02, T:0.22
Consensus pattern (26 bp):
AAACATTAACAAAAATACAATAAAAT
Found at i:1124496 original size:29 final size:29
Alignment explanation
Indices: 1124463--1124523 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
1124453 CAAAATAAAC
* *
1124463 AAAATCCAAAACGATGACCAAATTGAAAT
1 AAAATCCAAAACGATGACAAAATCGAAAT
* * * *
1124492 AAAATGCAATAGGATGTCAAAATCGAAAT
1 AAAATCCAAAACGATGACAAAATCGAAAT
1124521 AAA
1 AAA
1124524 TAAACAAAAC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.56, C:0.13, G:0.13, T:0.18
Consensus pattern (29 bp):
AAAATCCAAAACGATGACAAAATCGAAAT
Found at i:1127017 original size:2 final size:2
Alignment explanation
Indices: 1127010--1127054 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1127000 TTCTAACCCG
1127010 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1127052 TA T
1 TA T
1127055 GAAAGCATTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1128689 original size:200 final size:198
Alignment explanation
Indices: 1128302--1128775 Score: 589
Period size: 200 Copynumber: 2.4 Consensus size: 198
1128292 AAAATTTTGA
* * **
1128302 AAATTTACATATTACATTATACTTATGGGTTTCGATGTTTTTCCGGGATCGATACTTTTATAAAT
1 AAATTTACCTATTACATTATAATTATCAGTTTCGATGTTTTT--GGGATCGATACTTTTATAAAT
* * * * *
1128367 GTATCGACACTTTATGGTTGCACCCTTTTTTGTATTCATTCTGACCAAACGTATCGACACAAATT
64 GTATCGACACTTTATGGTTGCACCCGTTTGTGCATTCATCCTGACCAAAAGTATCGACACAAATT
* * * * *
1128432 TAGCAAGTGTCGATACTTTATGCTGACATATTTTATCATAAAACCGGTATATTTATATCGGTTAC
129 TAACAAGTATCGATACATTATGCTGACATATTTTATAATAAAACCGATATATTTATATCGGTTAC
1128497 ATTGT
194 ATTGT
* *
1128502 AAATTTACCTAATACGTTATAATTATCAGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATG
1 AAATTTACCTATTACATTATAATTATCAGTTTCGATGTTTTTGGGATCGATACTTTT-ATAAATG
*
1128567 TATCGACATTTTATGCG-TGCACCTCGTTTGTGCATTCATCCTGGA-CAATAAGTATCGACACAA
65 TATCGACACTTTATG-GTTGCACC-CGTTTGTGCATTCATCCT-GACCAA-AAGTATCGACACAA
* * *
1128630 A-TTACACAAGTATCGATACATTATGTTGACATATTTTCTAAT-TAACCGATATATTTATATCGG
126 ATTTA-ACAAGTATCGATACATTATGCTGACATATTTTATAATAAAACCGATATATTTATATCGG
1128693 TTACATTGT
190 TTACATTGT
* ** * *
1128702 TAATTTACCTATTACATTATAATTATTTGTTTTGATGTTTTTTGGG-TCGATACTTGTATAAAAT
1 AAATTTACCTATTACATTATAATTATCAGTTTCGATG-TTTTTGGGATCGATACTTTTAT-AAAT
*
1128766 GTATAGACAC
64 GTATCGACAC
1128776 ATATTTAGGT
Statistics
Matches: 237, Mismatches: 29, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
198 15 0.06
199 29 0.12
200 138 0.58
201 55 0.23
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (198 bp):
AAATTTACCTATTACATTATAATTATCAGTTTCGATGTTTTTGGGATCGATACTTTTATAAATGT
ATCGACACTTTATGGTTGCACCCGTTTGTGCATTCATCCTGACCAAAAGTATCGACACAAATTTA
ACAAGTATCGATACATTATGCTGACATATTTTATAATAAAACCGATATATTTATATCGGTTACAT
TGT
Found at i:1131629 original size:199 final size:198
Alignment explanation
Indices: 1131287--1131824 Score: 726
Period size: 199 Copynumber: 2.7 Consensus size: 198
1131277 ACAAAGTGTC
* * *
1131287 GATACATGTTGTAGACCTATTCTCTCATAAAATCGGTATATTTATATCGGTTATATTACAAAATT
1 GATACATGTTATAGACCTATTCTCTCATAAAACCGGTAT-TTTATACCGGTTATATTA-AAAATT
* * * *
1131352 ACCTATTATATTATAATTATGGGTTTCGATGTTTTCGGTATCGACACTTTTAATAAATGTATCAA
64 ACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTTTAATAAATGTATCGA
* * *
1131417 CACTTTGTGCGTTCATCC-TTTTTGGCATCCATTCTGGA-AAAAAATATCGACACAA-ATTTAAC
129 CACTTTATGCGTTCA-CCTTTTTTGGAATCCATTCTAGACAAAAAATATCGACACAATA-TTAAC
1131479 AACTGTA
192 AACTGTA
* * * *
1131486 GCTACATGTTATAGACCTATTCTCTCATAAAACCGGTATTTTTATACCGGTTACATTGTAAATTT
1 GATACATGTTATAGACCTATTCTCTCATAAAACCGGTA-TTTTATACCGGTTATATT-AAAAATT
* * *
1131551 ACCTATTACATTATAATTATGGGTTTTGATGTTTTTGGGATCGACACTTTTTGA-AAATATATCG
64 ACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACAC-TTTTAATAAATGTATCG
* * *
1131615 ACACTTTATGCGTTCACCTTTTTTGGAATCCATTCTAGACAAAAATTGTCGACACAATATTAATA
128 ACACTTTATGCGTTCACCTTTTTTGGAATCCATTCTAGACAAAAAATATCGACACAATATTAACA
* *
1131680 AGTGTC
193 ACTGTA
* *
1131686 GATACATATTATAGACCTATTCTCTCATAAAACCGGTA-TATATACCGGTTATATTAAAAATTAC
1 GATACATGTTATAGACCTATTCTCTCATAAAACCGGTATTTTATACCGGTTATATTAAAAATTAC
* * * *
1131750 CTATTACATTATAATTATGGGTTTCAATGTTTTTGAGATCGACACTTATAATAAATGTATCGAAA
66 CTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTTTAATAAATGTATCGACA
1131815 CTTTATGCGT
131 CTTTATGCGT
1131825 GCAACCCTTT
Statistics
Matches: 297, Mismatches: 35, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
196 4 0.01
197 70 0.24
198 17 0.06
199 139 0.47
200 66 0.22
201 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (198 bp):
GATACATGTTATAGACCTATTCTCTCATAAAACCGGTATTTTATACCGGTTATATTAAAAATTAC
CTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTTTAATAAATGTATCGACA
CTTTATGCGTTCACCTTTTTTGGAATCCATTCTAGACAAAAAATATCGACACAATATTAACAACT
GTA
Found at i:1132070 original size:249 final size:249
Alignment explanation
Indices: 1131583--1132032 Score: 629
Period size: 248 Copynumber: 1.8 Consensus size: 249
1131573 GTTTTGATGT
* * *
1131583 TTTTGGGATCGACACTTTTTGAAAATATATCGACACTTTATGCGTTCACCTTTTTTGGAATCCAT
1 TTTTGGGATCGACACTCTATGAAAATATATCGACACTTTATGCGTTCACCCTTTTTGGAATCCAT
* * * * *
1131648 TCTAGACAAAAATTGTCGACACAATATTAATAAGTGTCGATACATATTATAGACCTATTCTCTCA
66 TCTAGACAAAAAGTATCGACACAATACTAATAAGTGTCGATAAATATTATAGACATATTCTCTCA
* * *
1131713 TAAAACCGGTATATATACCGGTTATATTAAAAATTACCTATTACATTATAATTATGGGTTTCAAT
131 TAAAACCGGTATATATACCGATTACATTAAAAATTACCCATTACATTATAATTATGGGTTTCAAT
*
1131778 GTTTTTGAGATCGACACTTATAATAAATGTATCGAAACTTTATGCGTGCAACCC
196 GTTTTTGAGATCGACACTTATAATAAATGGATCGAAACTTTATGCGTGCAACCC
* * * **
1131832 TTTT-GGATTGACACTCTATGAAAATGTATCGACACTTTGTAG-GTTCACCCTTTTTGTCATCCA
1 TTTTGGGATCGACACTCTATGAAAATATATCGACACTTTAT-GCGTTCACCCTTTTTGGAATCCA
* * * *
1131895 TTCTGGACAAAAAGTATC-ACACAATACTAATAAGTGTCGATAAATGTTGTAGACATATT-TTTC
65 TTCTAGACAAAAAGTATCGACACAATACTAATAAGTGTCGATAAATATTATAGACATATTCTCTC
*
1131958 ATAAAACCGGTATATTTATATCGATTACATTGAAAAATTACCCATTACATTATAATTATGGGTTT
130 ATAAAACCGGTATA--TATACCGATTACATT-AAAAATTACCCATTACATTATAATTATGGGTTT
*
1132023 CGATGTTTTT
192 CAATGTTTTT
1132033 TGGGTCGTTA
Statistics
Matches: 175, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
246 17 0.10
247 36 0.21
248 76 0.43
249 46 0.26
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (249 bp):
TTTTGGGATCGACACTCTATGAAAATATATCGACACTTTATGCGTTCACCCTTTTTGGAATCCAT
TCTAGACAAAAAGTATCGACACAATACTAATAAGTGTCGATAAATATTATAGACATATTCTCTCA
TAAAACCGGTATATATACCGATTACATTAAAAATTACCCATTACATTATAATTATGGGTTTCAAT
GTTTTTGAGATCGACACTTATAATAAATGGATCGAAACTTTATGCGTGCAACCC
Found at i:1133344 original size:15 final size:15
Alignment explanation
Indices: 1133324--1133359 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
1133314 ACTTGTTTGG
1133324 ATCATCATCGTCATC
1 ATCATCATCGTCATC
1133339 ATCATCATCGTCATC
1 ATCATCATCGTCATC
*
1133354 TTCATC
1 ATCATC
1133360 TTCATTGGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.25, C:0.33, G:0.06, T:0.36
Consensus pattern (15 bp):
ATCATCATCGTCATC
Found at i:1135329 original size:201 final size:198
Alignment explanation
Indices: 1134813--1135353 Score: 838
Period size: 194 Copynumber: 2.7 Consensus size: 198
1134803 TATTTAAATT
* * *
1134813 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTACACATATTCTATCATAAAACCGGT
1 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGAC-TATTCTCTCATAAAATCGGT
*
1134878 ATATTTATACCTGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
65 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
1134943 GGATCGATACATTTTATAAATGTATCGACACTTTATGGTTCCCCCTTTTAGCATTCATTCTGGAC
130 GGATCGATACATTTTATAAATGTATCGACACTTTATGGTTCCCCCTTTTAGCATTCATTCTGGAC
1135008 CAAA
195 CAAA
*
1135012 CGTATCGACACAAAATTAAAAAAGTGTCGATACATG-T-T-GA-TATTCTCTCATAAAATCGGTA
1 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACTATTCTCTCATAAAATCGGTA
* * *
1135073 TATTTATATCGGTTACATTGAAAATTTATCTATTACATTATACTTATGGATGCATATGTTTCTAG
66 TATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTGG
* * * * *
1135138 GATCGATACTTTTTATAAATGTATCGACACTTTATTGTTGCACCCTTTTTGGCATTCATTCTTGA
131 GATCGATACATTTTATAAATGTATCGACACTTTATGGTT-C-CCCCTTTTAGCATTCATTCTGGA
1135203 CCAAA
194 CCAAA
* * **
1135208 AGTATCGACACAAAATTTAAAAAGTGTCAATACATGTTGTAGACCTATTCTCTCATAAAATCAAT
1 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGA-CTATTCTCTCATAAAATCGGT
* *
1135273 ATATTTATACCGGTTACATTGAAAATTTACCTCTTGCATTATACTTATGGATGCATATGTTTCTG
65 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
*
1135338 GGATCGATAAATTTTA
130 GGATCGATACATTTTA
1135354 CCTATTATAT
Statistics
Matches: 310, Mismatches: 25, Indels: 12
0.89 0.07 0.03
Matches are distributed among these distances:
194 117 0.38
195 1 0.00
196 59 0.19
197 2 0.01
198 2 0.01
199 37 0.12
201 92 0.30
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (198 bp):
AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACTATTCTCTCATAAAATCGGTA
TATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTGG
GATCGATACATTTTATAAATGTATCGACACTTTATGGTTCCCCCTTTTAGCATTCATTCTGGACC
AAA
Found at i:1135633 original size:19 final size:19
Alignment explanation
Indices: 1135609--1135653 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
1135599 TTACATTCAC
1135609 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCTT
1135628 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCTT
1135647 ATA-AAAA
1 ATACAAAA
1135654 AATTAACCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCTT
Found at i:1137315 original size:44 final size:42
Alignment explanation
Indices: 1137245--1137334 Score: 110
Period size: 44 Copynumber: 2.1 Consensus size: 42
1137235 CCATAGCCTC
* *
1137245 CTCTTTTATTTCACCCAATTGATCTCCTTCATCCAAGTCTTCAT
1 CTCTTTTATTTCACCC-ATTAATCTCCTTCA-CCAAGTATTCAT
*
1137289 CTCTTTTATTTCACCC-TTCAATTCTCCTTCACCAAGTATTGAT
1 CTCTTTTATTTCACCCATT-AA-TCTCCTTCACCAAGTATTCAT
1137332 CTC
1 CTC
1137335 CTTTCCACCA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
42 2 0.05
43 14 0.34
44 25 0.61
ACGTcount: A:0.20, C:0.32, G:0.04, T:0.43
Consensus pattern (42 bp):
CTCTTTTATTTCACCCATTAATCTCCTTCACCAAGTATTCAT
Found at i:1137441 original size:33 final size:33
Alignment explanation
Indices: 1137395--1137460 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
1137385 CATATTAAGA
*
1137395 TCACCCCTTAACACCT-TAACTTCTTTCACCACT
1 TCACCCCTCAACACCTCT-ACTTCTTTCACCACT
1137428 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1137461 CCATCTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.23, C:0.45, G:0.00, T:0.32
Consensus pattern (33 bp):
TCACCCCTCAACACCTCTACTTCTTTCACCACT
Found at i:1137519 original size:21 final size:21
Alignment explanation
Indices: 1137494--1137537 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1137484 CCCCTTATGC
1137494 CTCTCAAGTGTATCTTCAACT
1 CTCTCAAGTGTATCTTCAACT
* * *
1137515 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCAACT
1137536 CT
1 CT
1137538 TGATTGTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.32, G:0.09, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCAACT
Found at i:1137640 original size:15 final size:15
Alignment explanation
Indices: 1137620--1137652 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1137610 ACTCTGTTTT
1137620 CCCTCACCGTCATCC
1 CCCTCACCGTCATCC
*
1137635 CCCTCACTGTCATCC
1 CCCTCACCGTCATCC
1137650 CCC
1 CCC
1137653 AATACAACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.61, G:0.06, T:0.21
Consensus pattern (15 bp):
CCCTCACCGTCATCC
Found at i:1140068 original size:182 final size:181
Alignment explanation
Indices: 1139735--1140210 Score: 625
Period size: 182 Copynumber: 2.6 Consensus size: 181
1139725 AGTACTTATG
* * *
1139735 AAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTA-CGATTTTATCATTTCGATACCGGTTT
* * * *
1139800 TATAATATTTTTACATGTTATATCGTTGTGGATCGATATATTTTTATAAAGTATCGACACTTTAT
65 TATCATATTTTTACCTGTTATATCATTGTGGATCGATACATTTTTATAAAGTATCGACACTTTAT
* *
1139865 AAGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATT
130 AAGCACTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCAATACTTATATT
* * *
1139917 AAAGTACCGACACTTTAAATATATCCGGTAGCTCTTTATCGATTTTATCATTTCGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTA-CGATTTTATCATTTCGATACCGGTTT
*
1139982 TGTCATATTTTTACCTGTTATATCATTGTGGATCGATACATTTTTATAAAGTATCGACACTTTAT
65 TATCATATTTTTACCTGTTATATCATTGTGGATCGATACATTTTTATAAAGTATCGACACTTTAT
* * * * *
1140047 AGGCATTAAAATTGTTTCTCTTTTAAATTCACAAAGTGTCAATCCTTATATT
130 AAGCACTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCAATACTTATATT
* * * ** *
1140099 AAAGTATCGACACGTTCAATATATCCGGTAAG-GATTTACAGATATTGCCTTTTCG-TGACCGGT
1 AAAGTATCGACACTTTCAATATATCCGGT-AGCGCTTTAC-GATTTTATCATTTCGAT-ACCGGT
* * *
1140162 TTTATCGATATTTTTACCTGTTATATTGA-TATGAATCGATACATTTTTA
63 TTTATC-ATATTTTTACCTGTTATA-TCATTGTGGATCGATACATTTTTA
1140211 ATTTGGATCG
Statistics
Matches: 257, Mismatches: 32, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
181 2 0.01
182 215 0.84
183 38 0.15
184 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (181 bp):
AAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACGATTTTATCATTTCGATACCGGTTTT
ATCATATTTTTACCTGTTATATCATTGTGGATCGATACATTTTTATAAAGTATCGACACTTTATA
AGCACTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCAATACTTATATT
Found at i:1141331 original size:182 final size:182
Alignment explanation
Indices: 1141015--1141482 Score: 674
Period size: 182 Copynumber: 2.6 Consensus size: 182
1141005 TGAAAGTATA
* * *
1141015 GACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTATCATTTTGATACCGGTTTTATAATAT
1 GACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTCGATACCGGTTTTATCATAT
* *
1141080 TTTTACTTGTTATATCATTTTGGATCGATACATTTTTATAAAGTATCGACACTTTATAAGCGCTA
66 TTTTACTTGTTATATTATTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAAGCGCTA
*
1141145 AAACTGCTTT-TCTTTTAAATTCACAAAGTGTCGATACTTATATTAAAGTACC
131 AAACTG-TTTCTCTTTTAAATTCACAAAGTGTCGATACTTAGATTAAAGTACC
* * * *
1141197 GACACTTTAAATATATTCGGTAGCTCTTTACCGGTTTTATCATTTCGATACCGGTTTTGTCATAT
1 GACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTCGATACCGGTTTTATCATAT
* * *
1141262 TTTTACTTGTTATATTATTGTGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCGTTA
66 TTTTACTTGTTATATTATTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAAGCGCTA
* *
1141327 AAACTGTTTCTCTTTTAAATTCACAAAGTGTCGATCCTTAGATTAAAGTATC
131 AAACTGTTTCTCTTTTAAATTCACAAAGTGTCGATACTTAGATTAAAGTACC
* * * * *
1141379 GACACGTTCAATATATCCGGTAAG-GATTTACCGGTATTGTCTTTTCG-TGACCGGTTTTATCGA
1 GACACTTTCAATATATCCGGT-AGCGCTTTACCGGTTTTATCATTTCGAT-ACCGGTTTTATC-A
*
1141442 TATTTTTACATGTTATATTGA-TATGGATCGATACATTTTTA
63 TATTTTTACTTGTTATATT-ATTATGGATCGATACATTTTTA
1141483 ATTTGGATCG
Statistics
Matches: 256, Mismatches: 25, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
181 4 0.02
182 211 0.82
183 40 0.16
184 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.42
Consensus pattern (182 bp):
GACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTCGATACCGGTTTTATCATAT
TTTTACTTGTTATATTATTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAAGCGCTA
AAACTGTTTCTCTTTTAAATTCACAAAGTGTCGATACTTAGATTAAAGTACC
Found at i:1142594 original size:181 final size:181
Alignment explanation
Indices: 1142265--1142739 Score: 673
Period size: 181 Copynumber: 2.6 Consensus size: 181
1142255 CGTACTTATG
* ** *
1142265 AAAGTATCAACACTTTAAATATATTTGGTAGCGCTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAGCGCTTTACCGGTTTTATCA-TTTCATACCGGTTT
* *
1142330 TATCATATTTTTACATGTTATATCGTTGTGGATCGATGCATTTTTATAAAGTATCGACACTTTAT
65 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACTTTAT
*
1142395 AAGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGGTACTTATATT
130 AAGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATT
* *
1142447 AAAGTACCGACACTTTAAATATATCCGGTAGCTCTTTACCGGTTTTATCATTTCATACCGGTTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTCATACCGGTTTT
1142512 ATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACTTTATA
66 ATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACTTTATA
* * * *
1142577 GGCGTTAAAATTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
131 AGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATT
* * * * * * * **
1142628 AAAGTATCGACACATTCAATATATCCGATAAG-GATTTACCGGTATTGTCTTTTTGTGACCGGTT
1 AAAGTATCGACACTTTAAATATATCCGGT-AGCGCTTTACCGGTTTTATCATTTCAT-ACCGGTT
* * * *
1142692 TTATCGATATTTTTACCTATTATATTGATATGGATCGATACATTTTTA
64 TTATC-ATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTA
1142740 ATTTAGATCG
Statistics
Matches: 262, Mismatches: 28, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
181 165 0.63
182 59 0.23
183 38 0.15
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (181 bp):
AAAGTATCGACACTTTAAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTCATACCGGTTTT
ATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACTTTATA
AGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATT
Found at i:1143707 original size:3 final size:3
Alignment explanation
Indices: 1143699--1143761 Score: 117
Period size: 3 Copynumber: 20.7 Consensus size: 3
1143689 GAGACCATTA
1143699 TTG TTG TTG TTG TTG TTG TTG TTG TTTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG -TTG TTG TTG TTG TTG TTG TTG
1143745 TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TT
1143762 ATTTTATTTA
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 56 0.95
4 3 0.05
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:1143899 original size:49 final size:49
Alignment explanation
Indices: 1143827--1143920 Score: 127
Period size: 49 Copynumber: 1.9 Consensus size: 49
1143817 CTAGCCCTAT
* * *
1143827 CACGGTAGCCCTGCTGCACCAGTCCCCTACCA-CCTCCATTTCCACCAAC
1 CACGGTAACCCTACTACACCAGTCCCCTACCATCCT-CATTTCCACCAAC
* *
1143876 CACGGTAACCCTACTACACCAGTCCCCTTCCATCGTCATTTCCAC
1 CACGGTAACCCTACTACACCAGTCCCCTACCATCCTCATTTCCAC
1143921 TAATTCTGTC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
49 37 0.95
50 2 0.05
ACGTcount: A:0.21, C:0.47, G:0.11, T:0.21
Consensus pattern (49 bp):
CACGGTAACCCTACTACACCAGTCCCCTACCATCCTCATTTCCACCAAC
Found at i:1145237 original size:23 final size:24
Alignment explanation
Indices: 1145211--1145260 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1145201 TCTAGTCCTA
* *
1145211 TTTGCAT-TTTTTTTATTTTAATT
1 TTTGCATGTTCTTTTATGTTAATT
*
1145234 TTTGCATGTTCTTTTATGTTATTT
1 TTTGCATGTTCTTTTATGTTAATT
1145258 TTT
1 TTT
1145261 TAGTAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.14, C:0.06, G:0.08, T:0.72
Consensus pattern (24 bp):
TTTGCATGTTCTTTTATGTTAATT
Found at i:1146899 original size:21 final size:22
Alignment explanation
Indices: 1146857--1146901 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1146847 GGAGTGAGAA
1146857 ACTACTCCCTCGTGTGGTTTTC
1 ACTACTCCCTCGTGTGGTTTTC
1146879 ACTACTCCCTCGTGT-GTTTTC
1 ACTACTCCCTCGTGTGGTTTTC
1146900 AC
1 AC
1146902 CTCTGTACGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.11, C:0.33, G:0.16, T:0.40
Consensus pattern (22 bp):
ACTACTCCCTCGTGTGGTTTTC
Found at i:1156699 original size:11 final size:11
Alignment explanation
Indices: 1156683--1156754 Score: 53
Period size: 11 Copynumber: 6.5 Consensus size: 11
1156673 AAATCAAAAG
1156683 AATAAAAAGAA
1 AATAAAAAGAA
*
1156694 AATAAAAATAA
1 AATAAAAAGAA
1156705 AA-AAAAA-AA
1 AATAAAAAGAA
1156714 AATGAGGAAAAGAA
1 AAT-A--AAAAGAA
*
1156728 AGA-AAAGAGAA
1 A-ATAAAAAGAA
*
1156739 AAAAAAAAG-A
1 AATAAAAAGAA
1156749 AATAAA
1 AATAAA
1156755 TAAAAAGGGG
Statistics
Matches: 50, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
9 4 0.08
10 12 0.24
11 25 0.50
13 5 0.10
14 3 0.06
15 1 0.02
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.07
Consensus pattern (11 bp):
AATAAAAAGAA
Found at i:1156703 original size:17 final size:15
Alignment explanation
Indices: 1156664--1156760 Score: 52
Period size: 16 Copynumber: 5.8 Consensus size: 15
1156654 AGAAAAATTG
1156664 AAATGAAAAAAATCAAAA
1 AAAT-AAAAAAA--AAAA
*
1156682 GAATAAAAAGAAAATAA
1 AAATAAAAA-AAAA-AA
1156699 AAAT-AAAAAAAAAA
1 AAATAAAAAAAAAAA
1156713 AAATGAGGAAAAGAAAGAAA
1 AAAT-A--AAAA-AAA-AAA
* * *
1156733 AGAGAAAAAAAAAAG
1 AAATAAAAAAAAAAA
1156748 AAATAAATAAAAA
1 AAATAAA-AAAAA
1156761 GGGGTTCAAG
Statistics
Matches: 63, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 6 0.10
15 11 0.17
16 14 0.22
17 14 0.22
18 9 0.14
19 4 0.06
20 5 0.08
ACGTcount: A:0.79, C:0.01, G:0.11, T:0.08
Consensus pattern (15 bp):
AAATAAAAAAAAAAA
Found at i:1156724 original size:18 final size:17
Alignment explanation
Indices: 1156703--1156751 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
1156693 AAATAAAAAT
1156703 AAAAAAAAAAAAATGAGG
1 AAAAAAAAAAAAATGA-G
* *
1156721 AAAAGAAAGAAAA-GAG
1 AAAAAAAAAAAAATGAG
1156737 AAAAAAAAAAGAAAT
1 AAAAAAAAAA-AAAT
1156752 AAATAAAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 9 0.36
17 5 0.20
18 11 0.44
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (17 bp):
AAAAAAAAAAAAATGAG
Found at i:1158253 original size:134 final size:135
Alignment explanation
Indices: 1158048--1158356 Score: 396
Period size: 133 Copynumber: 2.3 Consensus size: 135
1158038 CATTTCAATG
* * * **
1158048 TCCCTAAAGAATAGTAGAA-TGAATCAACATTTCCAAATCT-AATTTCCTTGAAGAAACAGCTGA
1 TCCCTGAAGAACAGTAGAAGTGAATCAACATTTCCAGATCTGAATTTCCTTGAAGAAACAGAGGA
** * *
1158111 ACAAATCCCTTGTTTTTCCAGATTTGATCTTCCCTGAGGAA-CAGTAGAACAAGTCTGTCTCAAT
66 ACAAATCCC--AATTTTCCAGATTTGATCTTCCCTGAAGAAGCAGTAGAACAAGTCTGCCTCAAT
*
1158175 TCAATCT
129 TCAATAT
* * * *
1158182 TCCCTGAAGAACAGT-GAAGTGAATCAACATCTCTAGATCTGATTTTCCTTGAAGAATCAGAGGA
1 TCCCTGAAGAACAGTAGAAGTGAATCAACATTTCCAGATCTGAATTTCCTTGAAGAAACAGAGGA
* * *
1158246 A-AGATCCCAATTTTCCAGATTTGATCTTCCCTGAAGAAGCAGTGGGACAAGTCTGCCTCAATTC
66 ACAAATCCCAATTTTCCAGATTTGATCTTCCCTGAAGAAGCAGTAGAACAAGTCTGCCTCAATTC
1158310 AATAT
131 AATAT
*
1158315 TCCCTGAAGAACAGTGGAAG-GAATCAACATTTCCAGATCTGA
1 TCCCTGAAGAACAGTAGAAGTGAATCAACATTTCCAGATCTGA
1158357 CCTACCCTGA
Statistics
Matches: 152, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
132 27 0.18
133 64 0.42
134 41 0.27
135 20 0.13
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (135 bp):
TCCCTGAAGAACAGTAGAAGTGAATCAACATTTCCAGATCTGAATTTCCTTGAAGAAACAGAGGA
ACAAATCCCAATTTTCCAGATTTGATCTTCCCTGAAGAAGCAGTAGAACAAGTCTGCCTCAATTC
AATAT
Found at i:1160901 original size:217 final size:212
Alignment explanation
Indices: 1160615--1161048 Score: 682
Period size: 220 Copynumber: 2.0 Consensus size: 212
1160605 AAGTTAACAT
1160615 AATGTAATGTAATTTTTTAATGATGATATGACATTACGTTGGGACACATCAACATCACCATCACC
1 AATGTAATGTAATTTTTTAATGATGATATGACATTACGTTGGGACACATCAACATCACCATCACC
*
1160680 GTTAATTTTTTTATGACGAAATACC-AAA-AAATCTAAATTAAACAGTT-AAT-ATTTAAAAAAT
66 GTTAATTGTTTTATGACG--ATACCAAAAGAAATCTAAATTAAAC-GTTGAATAATTTAAAAAAT
1160741 AAATTTTGAGTATCAAAACAAAATAAAAGTAATAATTTATATACTAAACATGTAATATACCTCAA
128 AAATTTTGAGTATC-AAACAAAATAAAAGTAATAATTTATATACTAAACA-GTAATATACCTCAA
1160806 TTAAA-ATACAA-CAATTACTAA
191 TTAAATA-ACAATCAATTACTAA
*
1160827 AATGCTAATGTGATTTTTTTAATGATGATATGACATTACGTTATGGTGACACATCAACATCACCA
1 AATG-TAATGT-AATTTTTTAATGATGATATGACATTACG-T-TGG-GACACATCAACATCACCA
1160892 TCACCGTTAATTGTTTTATGACGATACCAAAATGAAATCTAAATTAAACGTTAGGAATAATTTAA
61 TCACCGTTAATTGTTTTATGACGATACCAAAA-GAAATCTAAATTAAACGTT--GAATAATTTAA
1160957 AAAATAAATTTTGAGTATCAAACAAAATAAAAGTAATAATTTATATACTAAACAGTAATATACCT
123 AAAATAAATTTTGAGTATCAAACAAAATAAAAGTAATAATTTATATACTAAACAGTAATATACCT
1161022 CAATTAAATAACAATCAATTACTAA
188 CAATTAAATAACAATCAATTACTAA
1161047 AA
1 AA
1161049 AAACAAAAGC
Statistics
Matches: 206, Mismatches: 2, Indels: 20
0.90 0.01 0.09
Matches are distributed among these distances:
212 4 0.02
213 6 0.03
214 27 0.13
215 6 0.03
216 6 0.03
217 43 0.21
218 15 0.07
219 23 0.11
220 51 0.25
221 25 0.12
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.32
Consensus pattern (212 bp):
AATGTAATGTAATTTTTTAATGATGATATGACATTACGTTGGGACACATCAACATCACCATCACC
GTTAATTGTTTTATGACGATACCAAAAGAAATCTAAATTAAACGTTGAATAATTTAAAAAATAAA
TTTTGAGTATCAAACAAAATAAAAGTAATAATTTATATACTAAACAGTAATATACCTCAATTAAA
TAACAATCAATTACTAA
Found at i:1164467 original size:15 final size:14
Alignment explanation
Indices: 1164442--1164471 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1164432 TGTTTGGTTT
1164442 GTGGTGGAGCTTGG
1 GTGGTGGAGCTTGG
1164456 GTGGTAGGAGCTTGG
1 GTGGT-GGAGCTTGG
1164471 G
1 G
1164472 GGCTCCTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.10, C:0.07, G:0.57, T:0.27
Consensus pattern (14 bp):
GTGGTGGAGCTTGG
Found at i:1165357 original size:9 final size:11
Alignment explanation
Indices: 1165266--1165492 Score: 80
Period size: 11 Copynumber: 20.6 Consensus size: 11
1165256 AAAAAATACA
*
1165266 ATATATATATT
1 ATATATAAATT
1165277 ATATATATAAGTT
1 ATATATA-AA-TT
1165290 -TATATAAA--
1 ATATATAAATT
*
1165298 CTATAT-AATT
1 ATATATAAATT
**
1165308 AT-TATAAGCT
1 ATATATAAATT
*
1165318 ATATACAAATT
1 ATATATAAATT
* *
1165329 ATGTGTATATGAACT
1 A----TATATAAATT
1165344 ATATATAAATT
1 ATATATAAATT
1165355 ATATATAAATT
1 ATATATAAATT
* *
1165366 ATATGTAAACT
1 ATATATAAATT
*
1165377 ATA-A-AAAGT
1 ATATATAAATT
**
1165386 ATATAGTTTA-T
1 ATATA-TAAATT
* *
1165397 AAACTATAATTT
1 ATA-TATAAATT
* *
1165409 ATATTTATATT
1 ATATATAAATT
*
1165420 A-ATATATATAT
1 ATATATAAAT-T
*
1165431 ATATATATATAT
1 ATATATAAAT-T
*
1165443 ATATATATATT
1 ATATATAAATT
*
1165454 ATATATATA-T
1 ATATATAAATT
*
1165464 ATATATATA-T
1 ATATATAAATT
*
1165474 ATATATATATAT
1 ATATATAAAT-T
1165486 ATATATA
1 ATATATA
1165493 TTAGTGAATG
Statistics
Matches: 169, Mismatches: 27, Indels: 39
0.72 0.11 0.17
Matches are distributed among these distances:
8 2 0.01
9 15 0.09
10 33 0.20
11 68 0.40
12 41 0.24
13 2 0.01
15 8 0.05
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.46
Consensus pattern (11 bp):
ATATATAAATT
Found at i:1165428 original size:2 final size:2
Alignment explanation
Indices: 1165408--1165493 Score: 142
Period size: 2 Copynumber: 44.5 Consensus size: 2
1165398 AACTATAATT
*
1165408 TA TA TT TA TA T- TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1165448 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1165489 TA TA T
1 TA TA T
1165494 TAGTGAATGG
Statistics
Matches: 79, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
1 3 0.04
2 76 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1165584 original size:19 final size:20
Alignment explanation
Indices: 1165560--1165597 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1165550 TTGATTTTAT
1165560 TTGGG-AATTTAGAGGGAAA
1 TTGGGAAATTTAGAGGGAAA
*
1165579 TTGGGAAATTTAGATGGAA
1 TTGGGAAATTTAGAGGGAA
1165598 TAGAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.37, C:0.00, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGGGAAATTTAGAGGGAAA
Found at i:1165826 original size:13 final size:13
Alignment explanation
Indices: 1165808--1165832 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1165798 CTATATATGT
1165808 ATATAAACTATAC
1 ATATAAACTATAC
1165821 ATATAAACTATA
1 ATATAAACTATA
1165833 TAAAATATAT
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:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (13 bp):
ATATAAACTATAC
Found at i:1166008 original size:21 final size:21
Alignment explanation
Indices: 1165970--1166031 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
1165960 AGTTTATAGA
*
1165970 AACCTTAAA-CCTTAAACTATG
1 AACCCTAAACCCTT-AACTATG
* *
1165991 AACCCTAAACCCTTAACTCTT
1 AACCCTAAACCCTTAACTATG
* * *
1166012 AATCCTAATCCCTGAACTAT
1 AACCCTAAACCCTTAACTAT
1166032 ATATGTAACT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
21 29 0.88
22 4 0.12
ACGTcount: A:0.37, C:0.31, G:0.03, T:0.29
Consensus pattern (21 bp):
AACCCTAAACCCTTAACTATG
Found at i:1166082 original size:22 final size:22
Alignment explanation
Indices: 1166057--1166106 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
1166047 TACATGTATG
* *
1166057 TATAAACTATGTATAATATA-TA
1 TATAAACTATATAT-ATAAACTA
*
1166079 TATAACCTATATATATAAACTA
1 TATAAACTATATATATAAACTA
1166101 TATAAA
1 TATAAA
1166107 GTAAATTACT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (22 bp):
TATAAACTATATATATAAACTA
Found at i:1166091 original size:13 final size:13
Alignment explanation
Indices: 1166073--1166104 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1166063 CTATGTATAA
*
1166073 TATATATATAACC
1 TATATATATAAAC
1166086 TATATATATAAAC
1 TATATATATAAAC
1166099 TATATA
1 TATATA
1166105 AAGTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (13 bp):
TATATATATAAAC
Found at i:1166355 original size:34 final size:34
Alignment explanation
Indices: 1166316--1166398 Score: 157
Period size: 34 Copynumber: 2.4 Consensus size: 34
1166306 AATGTAACAT
*
1166316 TAACCTATAGTCTATAAACAATAGTTAATATATA
1 TAACCTATAGTATATAAACAATAGTTAATATATA
1166350 TAACCTATAGTATATAAACAATAGTTAATATATA
1 TAACCTATAGTATATAAACAATAGTTAATATATA
1166384 TAACCTATAGTATAT
1 TAACCTATAGTATAT
1166399 GTATACATAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (34 bp):
TAACCTATAGTATATAAACAATAGTTAATATATA
Found at i:1166359 original size:20 final size:20
Alignment explanation
Indices: 1166336--1166394 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
1166326 TCTATAAACA
1166336 ATAGTTAATATATATAACCT
1 ATAGTTAATATATATAACCT
*
1166356 ATAG----TATATA-AA-CA
1 ATAGTTAATATATATAACCT
1166370 ATAGTTAATATATATAACCT
1 ATAGTTAATATATATAACCT
1166390 ATAGT
1 ATAGT
1166395 ATATGTATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
14 5 0.16
15 2 0.06
16 6 0.19
18 6 0.19
19 2 0.06
20 10 0.32
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.37
Consensus pattern (20 bp):
ATAGTTAATATATATAACCT
Found at i:1166363 original size:16 final size:16
Alignment explanation
Indices: 1166344--1166398 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 16
1166334 CAATAGTTAA
1166344 TATATATAACCTATAG
1 TATATATAACCTATAG
* *
1166360 TATATA-AACAATAGTTAA
1 TATATATAAC-CTA--TAG
1166378 TATATATAACCTATAG
1 TATATATAACCTATAG
1166394 TATAT
1 TATAT
1166399 GTATACATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
15 3 0.10
16 15 0.48
18 10 0.32
19 3 0.10
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.38
Consensus pattern (16 bp):
TATATATAACCTATAG
Found at i:1166403 original size:20 final size:19
Alignment explanation
Indices: 1166377--1166501 Score: 69
Period size: 20 Copynumber: 6.5 Consensus size: 19
1166367 ACAATAGTTA
*
1166377 ATATATATAACCTATA-GT
1 ATATATATAACCTATATAT
* * *
1166395 ATATGTAT-ACATATAAACT
1 ATATATATAACCTATATA-T
* *
1166414 ATATATGTAACTTATAGTACAT
1 ATATATATAACCTATA-T--AT
* * **
1166436 GTATGTATAAATTATATAT
1 ATATATATAACCTATATAT
*
1166455 AGTATATATAAAC--TATAT
1 A-TATATATAACCTATATAT
1166473 ATATATATAACCTATAGTAT
1 ATATATATAACCTATA-TAT
1166493 ATATATATA
1 ATATATATA
1166502 CAATCTCTTT
Statistics
Matches: 82, Mismatches: 15, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
17 16 0.20
18 13 0.16
19 11 0.13
20 27 0.33
21 1 0.01
22 13 0.16
23 1 0.01
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.41
Consensus pattern (19 bp):
ATATATATAACCTATATAT
Found at i:1166445 original size:35 final size:36
Alignment explanation
Indices: 1166377--1166455 Score: 97
Period size: 37 Copynumber: 2.2 Consensus size: 36
1166367 ACAATAGTTA
*
1166377 ATATATATAACCTATAGTATATGTATACATATAAACT
1 ATATATATAACCTATAGTACATGTATA-ATATAAACT
* * * *
1166414 ATATATGTAACTTATAGTACATGTAT-GTATAAATT
1 ATATATATAACCTATAGTACATGTATAATATAAACT
1166449 ATATATA
1 ATATATA
1166456 GTATATATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
35 13 0.36
37 23 0.64
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.41
Consensus pattern (36 bp):
ATATATATAACCTATAGTACATGTATAATATAAACT
Found at i:1168305 original size:21 final size:21
Alignment explanation
Indices: 1168275--1168328 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
1168265 AATCCTAACT
1168275 ATAAACCATAAACCCTAAAAC
1 ATAAACCATAAACCCTAAAAC
* ** *
1168296 ATAAATCATAAAGTCTAAACC
1 ATAAACCATAAACCCTAAAAC
*
1168317 ATAAACCCTAAA
1 ATAAACCATAAA
1168329 TTATACTTAC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.56, C:0.24, G:0.02, T:0.19
Consensus pattern (21 bp):
ATAAACCATAAACCCTAAAAC
Found at i:1168327 original size:14 final size:14
Alignment explanation
Indices: 1168251--1168328 Score: 52
Period size: 14 Copynumber: 5.6 Consensus size: 14
1168241 TTTTATAATG
1168251 AACCCTAAATCC-TA
1 AACCCTAAA-CCATA
* *
1168265 AATCCT-AACTATA
1 AACCCTAAACCATA
* *
1168278 AACCATAAACCCTA
1 AACCCTAAACCATA
* * *
1168292 AAACATAAATCATA
1 AACCCTAAACCATA
**
1168306 AAGTCTAAACCATA
1 AACCCTAAACCATA
1168320 AACCCTAAA
1 AACCCTAAA
1168329 TTATACTTAC
Statistics
Matches: 47, Mismatches: 15, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
12 1 0.02
13 8 0.17
14 38 0.81
ACGTcount: A:0.51, C:0.27, G:0.01, T:0.21
Consensus pattern (14 bp):
AACCCTAAACCATA
Found at i:1168419 original size:14 final size:14
Alignment explanation
Indices: 1168402--1168434 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1168392 CCTTATTCTA
1168402 TAAACTTTAAACCC
1 TAAACTTTAAACCC
*
1168416 TAAACTTTAAACCT
1 TAAACTTTAAACCC
1168430 TAAAC
1 TAAAC
1168435 ACCAAACCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
TAAACTTTAAACCC
Found at i:1168441 original size:21 final size:21
Alignment explanation
Indices: 1168402--1168441 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1168392 CCTTATTCTA
* * *
1168402 TAAACTTTAAACCCTAAACTT
1 TAAACCTTAAACACCAAACTT
1168423 TAAACCTTAAACACCAAAC
1 TAAACCTTAAACACCAAAC
1168442 CCTAATCCCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (21 bp):
TAAACCTTAAACACCAAACTT
Found at i:1171013 original size:137 final size:137
Alignment explanation
Indices: 1170757--1171048 Score: 512
Period size: 137 Copynumber: 2.1 Consensus size: 137
1170747 CAAACAAAAG
* * *
1170757 TCACGTAGGTGGCGCACTGTCCCTTGTTGTGCTTGGTGCTCTGTCTCTTGTTTTGTGTGTCTGCA
1 TCACGTGGGTGGCGCACTGTCCCTTGTTGTGCTTGGTGCACTGTCCCTTGTTTTGTGTGTCTGCA
*
1170822 GGGCATGAATTCGAGCATGGCCAGCATGGGCGACAATAGCATTGATTTCAGTGGATGGCTGACTA
66 GGGCATGAATTCGAGCATGGCCAGCATGGGCGACAATAGCATTGATTTCAGTGGATGGCTGACCA
1170887 GCATGGT
131 GCATGGT
1170894 TCACGTGGGTGGCGCACTGTCCCTTGTTGTGCTTGGTGCACTGTCCCTTGTTTTGTGTGTCTGCA
1 TCACGTGGGTGGCGCACTGTCCCTTGTTGTGCTTGGTGCACTGTCCCTTGTTTTGTGTGTCTGCA
* * * *
1170959 GGGCATGGATTCGAGCATGGCCAGCATGGGCGACAGTAGCATTGGTTTCGGTGGATGGCTGACCA
66 GGGCATGAATTCGAGCATGGCCAGCATGGGCGACAATAGCATTGATTTCAGTGGATGGCTGACCA
1171024 GCATGGT
131 GCATGGT
1171031 TCACGTGGGTGGCGCACT
1 TCACGTGGGTGGCGCACT
1171049 ATCTCGGGCT
Statistics
Matches: 147, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
137 147 1.00
ACGTcount: A:0.14, C:0.22, G:0.34, T:0.30
Consensus pattern (137 bp):
TCACGTGGGTGGCGCACTGTCCCTTGTTGTGCTTGGTGCACTGTCCCTTGTTTTGTGTGTCTGCA
GGGCATGAATTCGAGCATGGCCAGCATGGGCGACAATAGCATTGATTTCAGTGGATGGCTGACCA
GCATGGT
Found at i:1171334 original size:17 final size:17
Alignment explanation
Indices: 1171312--1171347 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1171302 TTCGAGTTTT
1171312 AGTTCGAGCTTGAATCG
1 AGTTCGAGCTTGAATCG
1171329 AGTTCGAGCTTGAATCG
1 AGTTCGAGCTTGAATCG
1171346 AG
1 AG
1171348 CTCAAAATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.28
Consensus pattern (17 bp):
AGTTCGAGCTTGAATCG
Found at i:1173231 original size:54 final size:54
Alignment explanation
Indices: 1173166--1173276 Score: 161
Period size: 54 Copynumber: 2.1 Consensus size: 54
1173156 CTTGGATGAG
* * *
1173166 AAATTATGAAAAT-ACTTCTATTAGGTAAAATTATGAAAATACCCTTATGTGGTA
1 AAATTACGAAAATAACCT-TATGAGGTAAAATTATGAAAATACCCTTATGTGGTA
* *
1173220 AAATTACGAAAATAACCTTATGGGGTAAAATTATGAAAATACCCTTATGTTGTA
1 AAATTACGAAAATAACCTTATGAGGTAAAATTATGAAAATACCCTTATGTGGTA
1173274 AAA
1 AAA
1173277 ATACAAGAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
54 48 0.94
55 3 0.06
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.32
Consensus pattern (54 bp):
AAATTACGAAAATAACCTTATGAGGTAAAATTATGAAAATACCCTTATGTGGTA
Found at i:1173274 original size:27 final size:27
Alignment explanation
Indices: 1173166--1173276 Score: 145
Period size: 27 Copynumber: 4.1 Consensus size: 27
1173156 CTTGGATGAG
*
1173166 AAATTATGAAAATA-CTTCTAT-TAGGTA
1 AAATTATGAAAATACCCT-TATGT-GGTA
1173193 AAATTATGAAAATACCCTTATGTGGTA
1 AAATTATGAAAATACCCTTATGTGGTA
* * *
1173220 AAATTACGAAAATAACCTTATGGGGTA
1 AAATTATGAAAATACCCTTATGTGGTA
*
1173247 AAATTATGAAAATACCCTTATGTTGTA
1 AAATTATGAAAATACCCTTATGTGGTA
1173274 AAA
1 AAA
1173277 ATACAAGAAT
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
27 71 0.96
28 3 0.04
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.32
Consensus pattern (27 bp):
AAATTATGAAAATACCCTTATGTGGTA
Found at i:1175661 original size:12 final size:12
Alignment explanation
Indices: 1175646--1175714 Score: 57
Period size: 12 Copynumber: 5.4 Consensus size: 12
1175636 GTGCACATGA
*
1175646 GTGTGCGTGTGC
1 GTGTGCGTGTGT
1175658 GTGTGCATGTGTGT
1 GTGTGC--GTGTGT
*
1175672 GTGCGCGTGTGT
1 GTGTGCGTGTGT
* *
1175684 GTGTCTGCATGGGT
1 GTG--TGCGTGTGT
*
1175698 GCGTGCGTGTGT
1 GTGTGCGTGTGT
1175710 GTGTG
1 GTGTG
1175715 TGAGAGAGAG
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
12 26 0.59
14 18 0.41
ACGTcount: A:0.03, C:0.13, G:0.48, T:0.36
Consensus pattern (12 bp):
GTGTGCGTGTGT
Found at i:1175673 original size:24 final size:24
Alignment explanation
Indices: 1175628--1175714 Score: 66
Period size: 26 Copynumber: 3.5 Consensus size: 24
1175618 ATGGGTACAT
* ** *
1175628 GTGTGCGCGTGCACATGAGTGTGC
1 GTGTGCGTGTGCATGTGTGTGTGC
1175652 GTGTGCGTGTGCATGTGTGTGTGCGC
1 GTGTGCGTGTGCATGTGTGTGT--GC
* * *
1175678 GTGTGTGTGTCTGCATGGGTGCGTGC
1 GTGTGCGTG--TGCATGTGTGTGTGC
*
1175704 GTGTGTGTGTG
1 GTGTGCGTGTG
1175715 TGAGAGAGAG
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
24 20 0.38
26 21 0.40
28 11 0.21
ACGTcount: A:0.06, C:0.15, G:0.46, T:0.33
Consensus pattern (24 bp):
GTGTGCGTGTGCATGTGTGTGTGC
Found at i:1175692 original size:28 final size:28
Alignment explanation
Indices: 1175652--1175715 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
1175642 ATGAGTGTGC
* * * *
1175652 GTGTGCGTGTGCATGTGTGTGTGCGCGT
1 GTGTGTGTCTGCATGGGTGCGTGCGCGT
*
1175680 GTGTGTGTCTGCATGGGTGCGTGCGTGT
1 GTGTGTGTCTGCATGGGTGCGTGCGCGT
1175708 GTGTGTGT
1 GTGTGTGT
1175716 GAGAGAGAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.03, C:0.12, G:0.47, T:0.38
Consensus pattern (28 bp):
GTGTGTGTCTGCATGGGTGCGTGCGCGT
Found at i:1176682 original size:16 final size:17
Alignment explanation
Indices: 1176632--1176683 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
1176622 TAAAAAATTA
1176632 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
1176649 GA-TT-AAA-TTAGGAGT
1 AATTTGAAAGTTA-GAGT
1176664 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
1176680 AATT
1 AATT
1176684 AAATCTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 8 0.28
16 11 0.38
17 4 0.14
18 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:1189780 original size:23 final size:24
Alignment explanation
Indices: 1189739--1189798 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
1189729 TGGTACATTA
1189739 GTGTACATTCTACGCGGCAC-TTAT
1 GTGTA-ATTCTACGCGGCACTTTAT
* * *
1189763 GTTTAATTCTATGTGGCACTTTAT
1 GTGTAATTCTACGCGGCACTTTAT
1189787 GTGTAATTCTAC
1 GTGTAATTCTAC
1189799 TATTTGTGCA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 12 0.40
24 18 0.60
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (24 bp):
GTGTAATTCTACGCGGCACTTTAT
Found at i:1194116 original size:6 final size:7
Alignment explanation
Indices: 1194100--1194129 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1194090 CTATCATTGC
1194100 TTTGTTT
1 TTTGTTT
1194107 TTTG-TT
1 TTTGTTT
1194113 TTTGTTT
1 TTTGTTT
1194120 TTTGTTT
1 TTTGTTT
1194127 TTT
1 TTT
1194130 TTACATTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (7 bp):
TTTGTTT
Found at i:1194118 original size:13 final size:13
Alignment explanation
Indices: 1194100--1194128 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1194090 CTATCATTGC
1194100 TTTGTTTTTTGTT
1 TTTGTTTTTTGTT
1194113 TTTGTTTTTTGTT
1 TTTGTTTTTTGTT
1194126 TTT
1 TTT
1194129 TTTACATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (13 bp):
TTTGTTTTTTGTT
Found at i:1196214 original size:34 final size:34
Alignment explanation
Indices: 1196175--1196241 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
1196165 TGAACATATA
* *
1196175 TAAACGAACATGTTCACGAATGTTAAATGAACAC
1 TAAACGAACATGCTCACGAATGTTAAACGAACAC
* **
1196209 TAAACGAACGTGCTCGTGAATGTTAAACGAACA
1 TAAACGAACATGCTCACGAATGTTAAACGAACA
1196242 TGTTCGCAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (34 bp):
TAAACGAACATGCTCACGAATGTTAAACGAACAC
Found at i:1196312 original size:23 final size:23
Alignment explanation
Indices: 1196284--1196351 Score: 91
Period size: 24 Copynumber: 2.9 Consensus size: 23
1196274 ACTTTTAAAC
*
1196284 GAACATTAAACAAACATGTTCAT
1 GAACATTAAACGAACATGTTCAT
* *
1196307 GAACATCCAAACGAATATGTTCAT
1 GAACAT-TAAACGAACATGTTCAT
*
1196331 GAACATTAAACGAACACGTTC
1 GAACATTAAACGAACATGTTC
1196352 GCAAACTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 18 0.47
24 20 0.53
ACGTcount: A:0.44, C:0.21, G:0.12, T:0.24
Consensus pattern (23 bp):
GAACATTAAACGAACATGTTCAT
Found at i:1199689 original size:26 final size:26
Alignment explanation
Indices: 1199651--1199710 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
1199641 TTATATTGTA
*
1199651 GCACAGAGGTGCTCAATCATCTTAAT
1 GCACAGAGCTGCTCAATCATCTTAAT
1199677 GCACAGAGCTGCTCAATCATCTTAAT
1 GCACAGAGCTGCTCAATCATCTTAAT
*
1199703 GCATAGAG
1 GCACAGAG
1199711 GTGTCAGATC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (26 bp):
GCACAGAGCTGCTCAATCATCTTAAT
Found at i:1199793 original size:55 final size:55
Alignment explanation
Indices: 1199677--1200022 Score: 356
Period size: 55 Copynumber: 6.3 Consensus size: 55
1199667 TCATCTTAAT
* * * * * * * *
1199677 GCACAGAGCTGCTCAATCA-TCTTA-ATGCATAGAGGTGTCAGATCCTAGATTGAA
1 GCACAGAGGTGCTCAATCAGTTTTAGCTACACAGAGGTGTCAGCT-CTTGGTTGAA
* * *
1199731 GCACAGAGGTGCTCAATCAATGTTAGCTACACAGAGGTGTCAGCTCTTGGCTGAA
1 GCACAGAGGTGCTCAATCAGTTTTAGCTACACAGAGGTGTCAGCTCTTGGTTGAA
* * * * * * *
1199786 GTACAGAGGTGCTCAGTCATTTTTAACTGCACAGAGGTGTCAGTTCTTGATTGAA
1 GCACAGAGGTGCTCAATCAGTTTTAGCTACACAGAGGTGTCAGCTCTTGGTTGAA
** *
1199841 GCACAGAGGTGCTCAATCAGTTTTAGCTACACAGAGGTGTCAGCTCTCCGCTGAA
1 GCACAGAGGTGCTCAATCAGTTTTAGCTACACAGAGGTGTCAGCTCTTGGTTGAA
* * * ** * * *
1199896 GTACAGAGGTGCTCAGTCATTTTTAATTGCACAGAGGTGTCAGTTCTCGGTTGAA
1 GCACAGAGGTGCTCAATCAGTTTTAGCTACACAGAGGTGTCAGCTCTTGGTTGAA
* * * *
1199951 GCACAGAGGTGCTCAATTC-GTTTTAGCTACATAGAGGTGTCAGCTTTTGATTGAT
1 GCACAGAGGTGCTCAA-TCAGTTTTAGCTACACAGAGGTGTCAGCTCTTGGTTGAA
1200006 GCACAGAGGTGCTCAAT
1 GCACAGAGGTGCTCAAT
1200023 TGCTAATTCT
Statistics
Matches: 240, Mismatches: 49, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
54 19 0.08
55 204 0.85
56 17 0.07
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (55 bp):
GCACAGAGGTGCTCAATCAGTTTTAGCTACACAGAGGTGTCAGCTCTTGGTTGAA
Found at i:1199844 original size:27 final size:25
Alignment explanation
Indices: 1199707--1199961 Score: 97
Period size: 28 Copynumber: 9.3 Consensus size: 25
1199697 CTTAATGCAT
*
1199707 AGAGGTGTCAGATCCTAGATTGAAGCAC
1 AGAGGTGTCAG-T-CTTG-TTGAAGCAC
* * *
1199735 AGAGGTGCTCAATCAATGTTAGCTA-CAC
1 AGAGGTG-TCAGTC-TTGTT-G-AAGCAC
* *
1199763 AGAGGTGTCAGCTCTTGGCTGAAGTAC
1 AGAGGTGTCAG-TCTT-GTTGAAGCAC
*
1199790 AGAGGTGCTCAGTCATT-TTTAACTGCAC
1 AGAGGTG-TCAGTC-TTGTTGAA--GCAC
1199818 AGAGGTGTCAGTTCTTGATTGAAGCAC
1 AGAGGTGTCAG-TCTTG-TTGAAGCAC
* *
1199845 AGAGGTGCTCAATCAGTT-TTAGCTA-CAC
1 AGAGGTG-TCAGTC--TTGTT-G-AAGCAC
* * *
1199873 AGAGGTGTCAGCTCTCCGCTGAAGTAC
1 AGAGGTGTCAG-TCT-TGTTGAAGCAC
*
1199900 AGAGGTGCTCAGTCATT-TTTAATTGCAC
1 AGAGGTG-TCAGTC-TTGTTGAA--GCAC
*
1199928 AGAGGTGTCAGTTCTCGGTTGAAGCAC
1 AGAGGTGTCAG-TCT-TGTTGAAGCAC
1199955 AGAGGTG
1 AGAGGTG
1199962 CTCAATTCGT
Statistics
Matches: 171, Mismatches: 26, Indels: 61
0.66 0.10 0.24
Matches are distributed among these distances:
26 9 0.05
27 71 0.42
28 76 0.44
29 15 0.09
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.27
Consensus pattern (25 bp):
AGAGGTGTCAGTCTTGTTGAAGCAC
Found at i:1199851 original size:110 final size:109
Alignment explanation
Indices: 1199679--1200020 Score: 472
Period size: 110 Copynumber: 3.1 Consensus size: 109
1199669 ATCTTAATGC
* * * * *
1199679 ACAGAGCTGCTCAATCA-TCTTAATGCATAGAGGTGTCAGATCCTAGATTGAAGCACAGAGGTGC
1 ACAGAGGTGCTCAGTCATTTTTAATGCACAGAGGTGTCAG-TTCTAGATTGAAGCACAGAGGTGC
* *
1199743 TCAATCAATGTTAGCTACACAGAGGTGTCAGCTCTTGGCTGAAGT
65 TCAATCAGTTTTAGCTACACAGAGGTGTCAGCTCTTGGCTGAAGT
*
1199788 ACAGAGGTGCTCAGTCATTTTTAACTGCACAGAGGTGTCAGTTCTTGATTGAAGCACAGAGGTGC
1 ACAGAGGTGCTCAGTCATTTTTAA-TGCACAGAGGTGTCAGTTCTAGATTGAAGCACAGAGGTGC
**
1199853 TCAATCAGTTTTAGCTACACAGAGGTGTCAGCTCTCCGCTGAAGT
65 TCAATCAGTTTTAGCTACACAGAGGTGTCAGCTCTTGGCTGAAGT
* *
1199898 ACAGAGGTGCTCAGTCATTTTTAATTGCACAGAGGTGTCAGTTCTCGGTTGAAGCACAGAGGTGC
1 ACAGAGGTGCTCAGTCATTTTTAA-TGCACAGAGGTGTCAGTTCTAGATTGAAGCACAGAGGTGC
* * ** * *
1199963 TCAATTC-GTTTTAGCTACATAGAGGTGTCAGCTTTTGATTGATGC
65 TCAA-TCAGTTTTAGCTACACAGAGGTGTCAGCTCTTGGCTGAAGT
1200008 ACAGAGGTGCTCA
1 ACAGAGGTGCTCA
1200021 ATTGCTAATT
Statistics
Matches: 209, Mismatches: 21, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
109 15 0.07
110 177 0.85
111 17 0.08
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (109 bp):
ACAGAGGTGCTCAGTCATTTTTAATGCACAGAGGTGTCAGTTCTAGATTGAAGCACAGAGGTGCT
CAATCAGTTTTAGCTACACAGAGGTGTCAGCTCTTGGCTGAAGT
Found at i:1206271 original size:16 final size:17
Alignment explanation
Indices: 1206250--1206290 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
1206240 TTATTTATTT
*
1206250 TTAATTTTTT-GAAAAG
1 TTAATTTTTTAAAAAAG
1206266 TTAATTTTTTAAAAAAG
1 TTAATTTTTTAAAAAAG
1206283 TATAATTT
1 T-TAATTT
1206291 CTTTTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.45
17 6 0.27
18 6 0.27
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (17 bp):
TTAATTTTTTAAAAAAG
Found at i:1206583 original size:16 final size:16
Alignment explanation
Indices: 1206540--1206587 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
1206530 AATCTGAACC
* * *
1206540 AAAAATAATTCAAATC
1 AAAAATAACTCGAATT
*
1206556 AAAAGTAACTCGAATT
1 AAAAATAACTCGAATT
1206572 AAAAATAACTCGAATT
1 AAAAATAACTCGAATT
1206588 GAAACTAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.25
Consensus pattern (16 bp):
AAAAATAACTCGAATT
Found at i:1209308 original size:23 final size:24
Alignment explanation
Indices: 1209270--1209318 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
1209260 TTGTCATTTG
* * *
1209270 AAATTTTATAAGTTTG-TTTTTTT
1 AAATTTTAAAAATTTGATATTTTT
1209293 AAATTTTAAAAATTTGATATTTTT
1 AAATTTTAAAAATTTGATATTTTT
1209317 AA
1 AA
1209319 TATAAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (24 bp):
AAATTTTAAAAATTTGATATTTTT
Found at i:1211669 original size:19 final size:19
Alignment explanation
Indices: 1211645--1211688 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1211635 ACATAAATAT
*
1211645 TGTATTCTTATGTTATAAA
1 TGTATTCTTATATTATAAA
* *
1211664 TGTATTGTTATATTGTAAA
1 TGTATTCTTATATTATAAA
*
1211683 TATATT
1 TGTATT
1211689 ATTTATTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (19 bp):
TGTATTCTTATATTATAAA
Found at i:1211795 original size:20 final size:20
Alignment explanation
Indices: 1211770--1211959 Score: 68
Period size: 20 Copynumber: 8.9 Consensus size: 20
1211760 TATTATAGTA
1211770 TTATAATATAAATAATATAT
1 TTATAATATAAATAATATAT
* * *
1211790 TTATAACATGAA-AATATGT
1 TTATAATATAAATAATATAT
*
1211809 TTATAAAAATAAGAATACAT-TAT
1 TTAT-AATAT-A-AATA-ATATAT
*
1211832 TTATTTAATA-AATTACTAATATAA
1 TTA--TAATATAA--A-TAATATAT
* *
1211856 TAATAATA-ATAATAATATGT
1 TTATAATATA-AATAATATAT
*
1211876 TTTTATATATTATAAT-ATATTAT
1 TTATA-ATA-TA-AATAATA-TAT
* *
1211899 TTATATTATCAAATGTTAATGT-T
1 TTATAATAT-AAA---TAATATAT
*
1211922 TTATAACATAAATAATATAT
1 TTATAATATAAATAATATAT
*
1211942 TTATAAAATAAATAATAT
1 TTATAATATAAATAATAT
1211960 TCGTATCTAA
Statistics
Matches: 127, Mismatches: 21, Indels: 44
0.66 0.11 0.23
Matches are distributed among these distances:
19 15 0.12
20 41 0.32
21 8 0.06
22 18 0.14
23 29 0.23
24 13 0.10
25 3 0.02
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (20 bp):
TTATAATATAAATAATATAT
Found at i:1214265 original size:60 final size:59
Alignment explanation
Indices: 1214133--1214244 Score: 172
Period size: 59 Copynumber: 1.9 Consensus size: 59
1214123 GTCGGGTGAT
*
1214133 CATTTTGTAACTTTTAATAGTTAGAGACTTAACAAAGTAACACCTTATAGTCAAAGGAC
1 CATTTTGTAACTTTTAATAGTTAGAGACTCAACAAAGTAACACCTTATAGTCAAAGGAC
* *
1214192 CATTTTGTAACTTTTAATAGTTGAGGGACTCAACAAAGTATCA-CTCTATAGTC
1 CATTTTGTAACTTTTAATAGTT-AGAGACTCAACAAAGTAACACCT-TATAGTC
1214245 GAGAGACTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
59 24 0.50
60 24 0.50
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (59 bp):
CATTTTGTAACTTTTAATAGTTAGAGACTCAACAAAGTAACACCTTATAGTCAAAGGAC
Found at i:1214647 original size:58 final size:57
Alignment explanation
Indices: 1214571--1214679 Score: 148
Period size: 58 Copynumber: 1.9 Consensus size: 57
1214561 TGGTCCTCTA
* * *
1214571 ACTAAAGGATATTACTTTGTTGAGTCTCCT-AACTATTAAAAGTTACAAAATGATCCCG
1 ACTAAAGGACATTACTTTGGTGAGTC-CCTCAA-TATTAAAAATTACAAAATGATCCCG
* *
1214629 ACTAAAGGACATTGCTTTGGTGAGTCCCTCGATATTAAAAATTACAAAATG
1 ACTAAAGGACATTACTTTGGTGAGTCCCTCAATATTAAAAATTACAAAATG
1214680 GTCATCCGAC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
57 21 0.47
58 24 0.53
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.31
Consensus pattern (57 bp):
ACTAAAGGACATTACTTTGGTGAGTCCCTCAATATTAAAAATTACAAAATGATCCCG
Found at i:1215218 original size:11 final size:11
Alignment explanation
Indices: 1215176--1215211 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
1215166 CTAAAAACTG
1215176 AACATATAAACA
1 AACAT-TAAACA
*
1215188 AACACTAAACA
1 AACATTAAACA
1215199 AACATTAAACA
1 AACATTAAACA
1215210 AA
1 AA
1215212 TGTTAAATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 18 0.82
12 4 0.18
ACGTcount: A:0.67, C:0.19, G:0.00, T:0.14
Consensus pattern (11 bp):
AACATTAAACA
Found at i:1215248 original size:22 final size:22
Alignment explanation
Indices: 1215182--1215251 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
1215172 ACTGAACATA
** * *
1215182 TAAACAAACACTAAACAAACAT
1 TAAACAAACGTTAAACGAACAC
*
1215204 TAAACAAATGTTAAATCTG--CAC
1 TAAACAAACGTTAAA-C-GAACAC
1215226 TAAACAAACGTTAAACGAACAC
1 TAAACAAACGTTAAACGAACAC
1215248 TAAA
1 TAAA
1215252 TGAACACATT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
20 1 0.03
21 1 0.03
22 35 0.92
23 1 0.03
ACGTcount: A:0.56, C:0.20, G:0.06, T:0.19
Consensus pattern (22 bp):
TAAACAAACGTTAAACGAACAC
Found at i:1215252 original size:33 final size:33
Alignment explanation
Indices: 1215190--1215252 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
1215180 TATAAACAAA
***
1215190 CACTAAACAAACATTAAACAAATGTTAAATCTG
1 CACTAAACAAACATTAAACAAACACTAAATCTG
* *
1215223 CACTAAACAAACGTTAAACGAACACTAAAT
1 CACTAAACAAACATTAAACAAACACTAAAT
1215253 GAACACATTC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.52, C:0.21, G:0.06, T:0.21
Consensus pattern (33 bp):
CACTAAACAAACATTAAACAAACACTAAATCTG
Found at i:1215276 original size:24 final size:23
Alignment explanation
Indices: 1215242--1215299 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 23
1215232 AACGTTAAAC
*
1215242 GAACACTAAATGAACACATTCAT
1 GAACAATAAATGAACACATTCAT
** *
1215265 GAACATATAAATGAACATGTTCGT
1 GAACA-ATAAATGAACACATTCAT
1215289 GAACAATAAAT
1 GAACAATAAAT
1215300 AAACTAATAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 11 0.37
24 19 0.63
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (23 bp):
GAACAATAAATGAACACATTCAT
Found at i:1223581 original size:28 final size:28
Alignment explanation
Indices: 1223512--1223591 Score: 69
Period size: 26 Copynumber: 3.0 Consensus size: 28
1223502 ACGATACATC
*
1223512 AAAAAAAATTAAAAAAC-ACTAAATAAT
1 AAAAAAAATTAAGAAACAACTAAATAAT
* * * *
1223539 -AAAAACATT-CG-AACAATTAAGTAAT
1 AAAAAAAATTAAGAAACAACTAAATAAT
*
1223564 AAAAAAAATTAAGAAACAAAATAAATAA
1 AAAAAAAATTAAGAAAC-AACTAAATAA
1223592 AATGTAAATA
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
24 3 0.08
25 8 0.21
26 16 0.41
27 1 0.03
28 3 0.08
29 8 0.21
ACGTcount: A:0.70, C:0.07, G:0.04, T:0.19
Consensus pattern (28 bp):
AAAAAAAATTAAGAAACAACTAAATAAT
Found at i:1223771 original size:3 final size:3
Alignment explanation
Indices: 1223763--1223807 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
1223753 CTCCTCACTC
* *
1223763 TCA TCA TCA TCA CCA TTA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1223808 GGAGCAGATA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:1225722 original size:26 final size:25
Alignment explanation
Indices: 1225692--1225772 Score: 78
Period size: 26 Copynumber: 3.1 Consensus size: 25
1225682 TCTCTCTCCT
1225692 AATATAATAAAAATTATATAAATTAA
1 AATATAATAAAAATTA-ATAAATTAA
*
1225718 AATATAAATTAATAA-TAATAAATT-A
1 AATAT-AA-TAAAAATTAATAAATTAA
1225743 AATA-AATAAAATATTAATAATAATTAA
1 AATATAATAAAA-ATTAAT-A-AATTAA
1225770 AAT
1 AAT
1225773 TAAAATAGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
22 4 0.09
23 3 0.07
24 4 0.09
25 6 0.13
26 16 0.35
27 8 0.17
28 5 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
AATATAATAAAAATTAATAAATTAA
Found at i:1225761 original size:30 final size:31
Alignment explanation
Indices: 1225717--1225776 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
1225707 ATATAAATTA
*
1225717 AAATATAAATTAATAATAA-T-AAATTAAAT
1 AAATAAAAATTAATAATAATTAAAATTAAAT
1225746 AAATAAAATATTAATAATAATTAAAATTAAA
1 AAATAAAA-ATTAATAATAATTAAAATTAAA
1225777 ATAGAATTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 7 0.26
30 11 0.41
31 1 0.04
32 8 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (31 bp):
AAATAAAAATTAATAATAATTAAAATTAAAT
Found at i:1225764 original size:14 final size:13
Alignment explanation
Indices: 1225695--1225765 Score: 62
Period size: 14 Copynumber: 5.5 Consensus size: 13
1225685 CTCTCCTAAT
1225695 ATAATAAAAATT-
1 ATAATAAAAATTA
1225707 AT-AT--AAATTA
1 ATAATAAAAATTA
*
1225717 A-AATATAAATTA
1 ATAATAAAAATTA
1225729 ATAATAATAAATTAA
1 ATAATAA-AAATT-A
1225744 ATAAATAAAATATTA
1 AT-AATAAAA-ATTA
1225759 ATAATAA
1 ATAATAA
1225766 TTAAAATTAA
Statistics
Matches: 49, Mismatches: 1, Indels: 16
0.74 0.02 0.24
Matches are distributed among these distances:
9 5 0.10
10 3 0.06
11 2 0.04
12 9 0.18
13 4 0.08
14 10 0.20
15 8 0.16
16 8 0.16
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
ATAATAAAAATTA
Found at i:1230644 original size:13 final size:13
Alignment explanation
Indices: 1230626--1230652 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1230616 TTACATACGC
1230626 ACATATGAAGACT
1 ACATATGAAGACT
1230639 ACATATGAAGACT
1 ACATATGAAGACT
1230652 A
1 A
1230653 TTCAACGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (13 bp):
ACATATGAAGACT
Found at i:1231631 original size:9 final size:9
Alignment explanation
Indices: 1231617--1231648 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
1231607 GATAAAAAAT
1231617 GAAAATAAA
1 GAAAATAAA
1231626 GAAAATAAA
1 GAAAATAAA
1231635 GAAAATAAA
1 GAAAATAAA
*
1231644 TAAAA
1 GAAAA
1231649 AATGATCGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.12
Consensus pattern (9 bp):
GAAAATAAA
Found at i:1231857 original size:25 final size:25
Alignment explanation
Indices: 1231816--1231863 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1231806 AAGAAGATAA
1231816 AAAAATAAAGATAAGGAAGAAAAAT
1 AAAAATAAAGATAAGGAAGAAAAAT
*
1231841 AAAAATGAA-ATAGAGGAAGAAAA
1 AAAAATAAAGATA-AGGAAGAAAA
1231864 GGGTAAATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.71, C:0.00, G:0.19, T:0.10
Consensus pattern (25 bp):
AAAAATAAAGATAAGGAAGAAAAAT
Found at i:1232709 original size:37 final size:37
Alignment explanation
Indices: 1232607--1232717 Score: 197
Period size: 36 Copynumber: 3.0 Consensus size: 37
1232597 ATGCTTATGG
1232607 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
*
1232644 ATCATATTTTTAGGA-TTTGAATCATAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
*
1232680 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
1232717 A
1 A
1232718 ACGTTATGTT
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
36 35 0.50
37 35 0.50
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
Found at i:1234002 original size:43 final size:43
Alignment explanation
Indices: 1233935--1234040 Score: 167
Period size: 43 Copynumber: 2.5 Consensus size: 43
1233925 ACTCAGTCGC
* *
1233935 TCATTTGCTGTAAAGTTGAGCTTGTGTTGTCTCGAGTCCAATA
1 TCATTCGCTGTAAAGTTGAACTTGTGTTGTCTCGAGTCCAATA
* *
1233978 TCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATA
1 TCATTCGCTGTAAAGTTGAACTTGTGTTGTCTCGAGTCCAATA
*
1234021 TCATTCGTTGTAAAGTTGAA
1 TCATTCGCTGTAAAGTTGAA
1234041 ATTGACTTGA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.39
Consensus pattern (43 bp):
TCATTCGCTGTAAAGTTGAACTTGTGTTGTCTCGAGTCCAATA
Found at i:1234120 original size:108 final size:109
Alignment explanation
Indices: 1233981--1234190 Score: 359
Period size: 108 Copynumber: 1.9 Consensus size: 109
1233971 TCCAATATCC
1233981 TTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCATTCGTTGTAAAGTTGAAATTGA
1 TTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCATTCGTTGTAAAGTTGAAATTGA
* *
1234046 CT-TGAATGAAATTGAAAAGTTGTTTGTTGATAGTCAGTCGCCA
66 CTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCGCCA
* * * *
1234089 TTCGTTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGA
1 TTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCATTCGTTGTAAAGTTGAAATTGA
1234154 CTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCA
66 CTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCA
1234191 ACTTGTCTCA
Statistics
Matches: 95, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
108 63 0.66
109 32 0.34
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (109 bp):
TTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCATTCGTTGTAAAGTTGAAATTGA
CTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCGCCA
Found at i:1234131 original size:151 final size:153
Alignment explanation
Indices: 1233856--1234148 Score: 455
Period size: 151 Copynumber: 1.9 Consensus size: 153
1233846 TTGTGTCGCT
* * * *
1233856 TCGAGTTCAATATCCTTTGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
1 TCGAGTCCAATATCATTCGCTGTAAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
* *
1233921 TTACACTCAGTCGCTCATTTGCTGTAAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGC
66 TGACACTCAGTCGCTCATTCGCTGTAAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGC
1233986 TGTGAAGTTGAACTTGTGTTGTC
131 TGTGAAGTTGAACTTGTGTTGTC
* *
1234009 TCGAGTCCAATATCATTCGTTGTAAAGTTGAAATTGACT-TGAATGAAATTGAAAAGTTGTTTGT
1 TCGAGTCCAATATCATTCGCTGTAAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
* * * * *
1234073 TGATAGTCAGTCGC-CATTCGTTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGT
66 TGACACTCAGTCGCTCATTCGCTGTAAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGC
1234137 TGTGAAGTTGAA
131 TGTGAAGTTGAA
1234149 ATTGACTCTG
Statistics
Matches: 127, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
151 58 0.46
152 35 0.28
153 34 0.27
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.38
Consensus pattern (153 bp):
TCGAGTCCAATATCATTCGCTGTAAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
TGACACTCAGTCGCTCATTCGCTGTAAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGC
TGTGAAGTTGAACTTGTGTTGTC
Found at i:1234742 original size:33 final size:32
Alignment explanation
Indices: 1234705--1234776 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
1234695 CATTAGGATT
* * *
1234705 TTGAATCCCCGAAGATGCCCCCAATATTCGATG
1 TTGAATCCCCAAAAATG-CCCCAACATTCGATG
** *
1234738 TTGAATTTCCAAAAATGCCCCAACATTTGATG
1 TTGAATCCCCAAAAATGCCCCAACATTCGATG
1234770 TTGAATC
1 TTGAATC
1234777 TTCAAATGTG
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
32 19 0.59
33 13 0.41
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (32 bp):
TTGAATCCCCAAAAATGCCCCAACATTCGATG
Found at i:1239137 original size:24 final size:25
Alignment explanation
Indices: 1239082--1239137 Score: 66
Period size: 24 Copynumber: 2.3 Consensus size: 25
1239072 AAATACAAAT
1239082 AAATAAAATAAATGTAAAGAAGATA
1 AAATAAAATAAATGTAAAGAAGATA
1239107 AAA-AAAATAAA-G-ATAAGAA-ATAA
1 AAATAAAATAAATGTA-AAGAAGAT-A
1239130 AAATAAAA
1 AAATAAAA
1239138 ATGAAATAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
22 3 0.11
23 10 0.36
24 12 0.43
25 3 0.11
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (25 bp):
AAATAAAATAAATGTAAAGAAGATA
Found at i:1239559 original size:17 final size:20
Alignment explanation
Indices: 1239524--1239560 Score: 53
Period size: 17 Copynumber: 2.0 Consensus size: 20
1239514 AAGTATATAT
1239524 AATAATAATAGTAAGAAAAA
1 AATAATAATAGTAAGAAAAA
1239544 AATAA-AATA-TAA-AAAAA
1 AATAATAATAGTAAGAAAAA
1239561 TTGAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.29
18 3 0.18
19 4 0.24
20 5 0.29
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (20 bp):
AATAATAATAGTAAGAAAAA
Found at i:1239951 original size:37 final size:37
Alignment explanation
Indices: 1239901--1240008 Score: 153
Period size: 37 Copynumber: 2.9 Consensus size: 37
1239891 TTATGGATCC
*
1239901 TATTTTTAAGAGTTTGAATCATAGTAAAACTCTATCA
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCA
* * * * *
1239938 TATTTTTGGGAGTTTGAATCATAGTAAAATTATTTCC
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCA
*
1239975 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTA
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTA
1240009 ACGTTATGTT
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (37 bp):
TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCA
Found at i:1241208 original size:29 final size:30
Alignment explanation
Indices: 1241127--1241212 Score: 79
Period size: 29 Copynumber: 2.9 Consensus size: 30
1241117 AAAATGTTTA
*
1241127 AAAAGTTTGCGGACTAATTTAGAATATAGGTC
1 AAAAGTTTGAGGACTAATTTA-AA-ATAGGTC
* * * *
1241159 -ATAGTTTGGGGA-TAAAATTAAAATA-TTC
1 AAAAGTTTGAGGACT-AATTTAAAATAGGTC
1241187 AAAAGTTTGAGGACTAATTTAAAATA
1 AAAAGTTTGAGGACTAATTTAAAATA
1241213 ATAGTTATAA
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
28 2 0.05
29 23 0.52
30 4 0.09
31 15 0.34
ACGTcount: A:0.43, C:0.06, G:0.19, T:0.33
Consensus pattern (30 bp):
AAAAGTTTGAGGACTAATTTAAAATAGGTC
Found at i:1241237 original size:60 final size:60
Alignment explanation
Indices: 1241108--1241271 Score: 161
Period size: 60 Copynumber: 2.7 Consensus size: 60
1241098 TACATTTTGT
* * * * * **
1241108 GATGAAATCAAAATGTTTAAAAAGTTTGCGGACTAATTTAGAATATAGGTCATAGTTTGGG
1 GATGAAATTAAAAT-ATTAAAAAGTTTGAGGACTAATTTAAAATATAGGTCATAATTTAAG
* * *
1241169 GATAAAATTAAAATATTCAAAAGTTTGAGGACTAATTTAAAATAATA-GTTATAATTTAAG
1 GATGAAATTAAAATATTAAAAAGTTTGAGGACTAATTTAAAAT-ATAGGTCATAATTTAAG
* * * *
1241229 GATGAAATTAACATATTTAAAAA-TTTAAAGAATAATTTAAAAT
1 GATGAAATTAAAATA-TTAAAAAGTTTGAGGACTAATTTAAAAT
1241272 GAGAATCATA
Statistics
Matches: 85, Mismatches: 16, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
60 64 0.75
61 21 0.25
ACGTcount: A:0.47, C:0.04, G:0.15, T:0.34
Consensus pattern (60 bp):
GATGAAATTAAAATATTAAAAAGTTTGAGGACTAATTTAAAATATAGGTCATAATTTAAG
Found at i:1243096 original size:50 final size:50
Alignment explanation
Indices: 1243021--1243120 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
1243011 TCATGGCTCG
1243021 CACCTTTCTGACACAATTTTAATGGCGATCGATGCCATTTATACGTATCA
1 CACCTTTCTGACACAATTTTAATGGCGATCGATGCCATTTATACGTATCA
1243071 CACCTTTCTGACACAATTTTAATGGCGATCGATGCCATTTATACGTATCA
1 CACCTTTCTGACACAATTTTAATGGCGATCGATGCCATTTATACGTATCA
1243121 GTTGTTGACC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (50 bp):
CACCTTTCTGACACAATTTTAATGGCGATCGATGCCATTTATACGTATCA
Found at i:1245363 original size:62 final size:62
Alignment explanation
Indices: 1245288--1245437 Score: 264
Period size: 62 Copynumber: 2.4 Consensus size: 62
1245278 AATGAAATTG
* * *
1245288 GGGATGAAATTAGAATATTCAAAAGTCAGGGGACTAATTTAAAAAGAGGGTCATATAGTTTA
1 GGGATGAACTTAGAATGTTCAAAAGTCAGGGGACCAATTTAAAAAGAGGGTCATATAGTTTA
*
1245350 GGGATGAACTTAGAATGTTCAAAAGTCAGGGGACCAATTTAAAAAGAGGGTTATATAGTTTA
1 GGGATGAACTTAGAATGTTCAAAAGTCAGGGGACCAATTTAAAAAGAGGGTCATATAGTTTA
1245412 GGGATGAACTTAGAATGTTCAAAAGT
1 GGGATGAACTTAGAATGTTCAAAAGT
1245438 TTAAAGGACT
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 84 1.00
ACGTcount: A:0.40, C:0.07, G:0.25, T:0.27
Consensus pattern (62 bp):
GGGATGAACTTAGAATGTTCAAAAGTCAGGGGACCAATTTAAAAAGAGGGTCATATAGTTTA
Found at i:1253499 original size:20 final size:21
Alignment explanation
Indices: 1253476--1253527 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1253466 ATTCTGACTA
1253476 TCGCATTGCGA-TTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
1253496 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
1253517 TCGCAATGCGA
1 TCGCATTGCGA
1253528 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:1253542 original size:20 final size:20
Alignment explanation
Indices: 1253517--1253580 Score: 112
Period size: 20 Copynumber: 3.2 Consensus size: 20
1253507 TTTTCCTAAT
*
1253517 TCGCAATGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
1253537 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
1253557 TCGCAACGCGAATACGT-AA
1 TCGCAACGCGAATACGTAAA
1253576 TCGCA
1 TCGCA
1253581 TTGCGATTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
19 7 0.16
20 36 0.84
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.17
Consensus pattern (20 bp):
TCGCAACGCGAATACGTAAA
Found at i:1253592 original size:20 final size:20
Alignment explanation
Indices: 1253475--1253609 Score: 71
Period size: 20 Copynumber: 6.8 Consensus size: 20
1253465 GATTCTGACT
**
1253475 ATCGCATTGCGATTT-CCAA
1 ATCGCATTGCGATTTACGTA
* * *
1253494 ATTCGCGTTGCGATTTTCCTA
1 A-TCGCATTGCGATTTACGTA
* *
1253515 ATTCGCAATGCGA-ATACGTAA
1 A-TCGCATTGCGATTTACGT-A
** *
1253536 ATCGCAACGCGA-ATACGTAA
1 ATCGCATTGCGATTTACGT-A
** *
1253556 ATCGCAACGCGA-ATACGTA
1 ATCGCATTGCGATTTACGTA
1253575 ATCGCATTGCGATTTACGTA
1 ATCGCATTGCGATTTACGTA
**
1253595 ATCGTGTTGCGATTT
1 ATCGCATTGCGATTT
1253610 TAGTAAATCG
Statistics
Matches: 99, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
19 12 0.12
20 71 0.72
21 16 0.16
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (20 bp):
ATCGCATTGCGATTTACGTA
Found at i:1253593 original size:40 final size:41
Alignment explanation
Indices: 1253496--1253595 Score: 114
Period size: 40 Copynumber: 2.5 Consensus size: 41
1253486 ATTTCCAAAT
* * * * *
1253496 TCGCGTTGCGATTTTCCTAATTCGCAATGCGAATACGTAAA
1 TCGCATTGCGATTTACGTAAATCGCAACGCGAATACGTAAA
** *
1253537 TCGCAACGCGA-ATACGTAAATCGCAACGCGAATACGT-AA
1 TCGCATTGCGATTTACGTAAATCGCAACGCGAATACGTAAA
1253576 TCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAA
1253596 TCGTGTTGCG
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
39 11 0.23
40 28 0.60
41 8 0.17
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (41 bp):
TCGCATTGCGATTTACGTAAATCGCAACGCGAATACGTAAA
Found at i:1254535 original size:24 final size:24
Alignment explanation
Indices: 1254484--1254537 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1254474 GTATTCAAAA
*
1254484 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
1254508 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
1254532 TTTGAT
1 TTTGAT
1254538 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:1257101 original size:19 final size:19
Alignment explanation
Indices: 1257077--1257193 Score: 104
Period size: 19 Copynumber: 6.4 Consensus size: 19
1257067 GCAACGAGAG
1257077 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1257096 AATCGCAAAGCGAAACT-AA
1 AATCGCAATGCGAAA-TGAA
*
1257115 AATCGCAATGCGGAAATGAC
1 AATCGCAATGC-GAAATGAA
*
1257135 TATCGCAATGCGAAAT-AA
1 AATCGCAATGCGAAATGAA
* * *
1257153 AATCACAA--C--CA-GAG
1 AATCGCAATGCGAAATGAA
*
1257167 AATCGCATTGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1257186 AATCGCAA
1 AATCGCAA
1257194 CGAGGGAATC
Statistics
Matches: 75, Mismatches: 14, Indels: 18
0.70 0.13 0.17
Matches are distributed among these distances:
14 8 0.11
16 2 0.03
18 8 0.11
19 41 0.55
20 16 0.21
ACGTcount: A:0.46, C:0.20, G:0.19, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1257154 original size:38 final size:38
Alignment explanation
Indices: 1257077--1257156 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 38
1257067 GCAACGAGAG
1257077 AATCGCAATGCGAAATGAAAATCGCAAAGCGAAACTAA
1 AATCGCAATGCGAAATGAAAATCGCAAAGCGAAACTAA
** *
1257115 AATCGCAATGCGGAAATGACTATCGCAATGCGAAA-TAA
1 AATCGCAATGC-GAAATGAAAATCGCAAAGCGAAACTAA
1257153 AATC
1 AATC
1257157 ACAACCAGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 18 0.47
39 20 0.53
ACGTcount: A:0.46, C:0.19, G:0.19, T:0.16
Consensus pattern (38 bp):
AATCGCAATGCGAAATGAAAATCGCAAAGCGAAACTAA
Found at i:1257203 original size:33 final size:33
Alignment explanation
Indices: 1257136--1257228 Score: 116
Period size: 33 Copynumber: 2.8 Consensus size: 33
1257126 GGAAATGACT
* *
1257136 ATCGCAATGCGAAAT-AAAATCACAACCAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1257168 ATCGCATTGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
1257201 ATCGTAAAGCGAAATGAAAATTGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1257229 CGAATTTAGT
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
32 14 0.27
33 38 0.73
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1257250 original size:19 final size:21
Alignment explanation
Indices: 1257228--1257270 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
1257218 AAATTGCAAC
1257228 GCGAATT-TAGTTTCG-CGTT
1 GCGAATTATAGTTTCGTCGTT
1257247 GCG-ATTATAGTTTCGTCGTT
1 GCGAATTATAGTTTCGTCGTT
1257267 GCGA
1 GCGA
1257271 TTTTCATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 3 0.14
19 11 0.52
20 7 0.33
ACGTcount: A:0.16, C:0.16, G:0.28, T:0.40
Consensus pattern (21 bp):
GCGAATTATAGTTTCGTCGTT
Done.