Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008323.1 Hibiscus syriacus cultivar Beakdansim tig00111027_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: 5101972
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 22 of 26
Found at i:4391219 original size:23 final size:23
Alignment explanation
Indices: 4391186--4391243 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
4391176 TGTTCGACTC
*
4391186 GTTGCTTGTTAAGCTCATTGCTT
1 GTTGCTAGTTAAGCTCATTGCTT
*
4391209 GTTGCTCGTTAAGCTCATTGCTT
1 GTTGCTAGTTAAGCTCATTGCTT
4391232 GTTGCTAGTTAA
1 GTTGCTAGTTAA
4391244 ACTCGTCGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.16, C:0.17, G:0.22, T:0.45
Consensus pattern (23 bp):
GTTGCTAGTTAAGCTCATTGCTT
Found at i:4393808 original size:199 final size:201
Alignment explanation
Indices: 4393467--4393868 Score: 781
Period size: 199 Copynumber: 2.0 Consensus size: 201
4393457 TAATATGATC
4393467 GACATCAATCAAAAAATAAAATTAATACAACTAAATACATTTAAGGTTATTACATACATAAAATG
1 GACATCAATCAAAAAATAAAATTAATACAACTAAATACATTTAAGGTTATTACATACATAAAATG
4393532 ATCCTTTTAAGTAACGTGTTGTTTCGAAAGTGGACATTGTAAAAAATTAACAGAATCTATTTTTA
66 ATCCTTTTAAGTAACGTGTTGTTTCGAAAGTGGACATTGTAAAAAATTAACAGAATCTATTTTTA
4393597 TTAATTCTGATTATGAAACGTAAAAGTAAAGGTTGCAAATTTTCTTCGTTTGTTAGTATAT-AAA
131 TTAATTCTGATTATGAAACGTAAAAGTAAAGGTTGCAAATTTTCTTCGTTTGTTAGTATATAAAA
4393661 TTAGAT
196 TTAGAT
*
4393667 GACATCAATCAAAAAATAAAATTAATACAACTAAATACATTTAAGTTTATTACATACAT-AAATG
1 GACATCAATCAAAAAATAAAATTAATACAACTAAATACATTTAAGGTTATTACATACATAAAATG
4393731 ATCCTTTTAAGTAACGTGTTGTTTCGAAAGTGGACATTGTAAAAAATTAACAGAATCTATTTTTA
66 ATCCTTTTAAGTAACGTGTTGTTTCGAAAGTGGACATTGTAAAAAATTAACAGAATCTATTTTTA
4393796 TTAATTCTGATTATGAAACGTAAAAGTAAAGGTTGCAAATTTTCTTCGTTTGTTAGTATATAAAA
131 TTAATTCTGATTATGAAACGTAAAAGTAAAGGTTGCAAATTTTCTTCGTTTGTTAGTATATAAAA
4393861 TTAGAT
196 TTAGAT
4393867 GA
1 GA
4393869 ACTATTTTGT
Statistics
Matches: 200, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
199 131 0.65
200 69 0.34
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (201 bp):
GACATCAATCAAAAAATAAAATTAATACAACTAAATACATTTAAGGTTATTACATACATAAAATG
ATCCTTTTAAGTAACGTGTTGTTTCGAAAGTGGACATTGTAAAAAATTAACAGAATCTATTTTTA
TTAATTCTGATTATGAAACGTAAAAGTAAAGGTTGCAAATTTTCTTCGTTTGTTAGTATATAAAA
TTAGAT
Found at i:4395981 original size:66 final size:64
Alignment explanation
Indices: 4395875--4396001 Score: 227
Period size: 66 Copynumber: 2.0 Consensus size: 64
4395865 ACTTCTAAAG
*
4395875 AGAACAATATTATCCTTATCACTAAGATCACTTGATGAGATCATATATAGGTAGAGACTTAAAAC
1 AGAACAATATTATCCTTATCACTAAGACCACTTGATGAGATC--ATATAGGTAGAGACTTAAAAC
4395940 A
64 A
4395941 AGAACAATATTATCCTTATCACTAAGACCACTTGATGAGATCATATAGGTAGAGACTTAAA
1 AGAACAATATTATCCTTATCACTAAGACCACTTGATGAGATCATATAGGTAGAGACTTAAA
4396002 TTCATAACTA
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
64 19 0.32
66 41 0.68
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (64 bp):
AGAACAATATTATCCTTATCACTAAGACCACTTGATGAGATCATATAGGTAGAGACTTAAAACA
Found at i:4397263 original size:24 final size:24
Alignment explanation
Indices: 4397226--4397273 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
4397216 GAATTCCAAG
* * *
4397226 TAAAATTGAAAATATTTAATAAAA
1 TAAAATAGAAAATAATAAATAAAA
*
4397250 TAAAATAGATAATAATAAATAAAA
1 TAAAATAGAAAATAATAAATAAAA
4397274 GGGAAATAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (24 bp):
TAAAATAGAAAATAATAAATAAAA
Found at i:4398056 original size:73 final size:72
Alignment explanation
Indices: 4397903--4398049 Score: 197
Period size: 73 Copynumber: 2.0 Consensus size: 72
4397893 AAACATCTTA
* **
4397903 AATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAAATAATAATATTTAAAATA
1 AATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAAAAAATAATATAAAAAATA
4397968 ATATTCT
66 ATATTCT
*
4397975 AAATCCTAATTAAAATAC-TAAAACATATTTAAACTAAAATACCTAAAACAAAGATAGAATATAA
1 -AATCCTAATTAAAACACTTAAAAC-TATTTAAACTAAAATACCTAAAA-AAA-AT--AATATAA
4398039 AAAATAATATT
60 AAAATAATATT
4398050 ATCCTAAAAC
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
72 6 0.09
73 39 0.60
74 2 0.03
75 2 0.03
77 16 0.25
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.30
Consensus pattern (72 bp):
AATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAAAAAATAATATAAAAAATA
ATATTCT
Found at i:4399952 original size:5 final size:5
Alignment explanation
Indices: 4399938--4399992 Score: 83
Period size: 5 Copynumber: 10.8 Consensus size: 5
4399928 AGTTTGCTAA
* *
4399938 AAAAT AAAAT GAAAT AAAAT AAAAT AAAACA AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T AAAAT AAAAT AAAAT AAAAT
4399989 AAAA
1 AAAA
4399993 AATATAATGA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
5 41 0.91
6 4 0.09
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:4399973 original size:21 final size:21
Alignment explanation
Indices: 4399949--4399993 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
4399939 AAATAAAATG
4399949 AAATAAAATAAAATAAAACAA
1 AAATAAAATAAAATAAAACAA
*
4399970 AAATAAAATAAAATAAAATAA
1 AAATAAAATAAAATAAAACAA
4399991 AAA
1 AAA
4399994 ATATAATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.82, C:0.02, G:0.00, T:0.16
Consensus pattern (21 bp):
AAATAAAATAAAATAAAACAA
Found at i:4399973 original size:26 final size:26
Alignment explanation
Indices: 4399943--4399992 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
4399933 GCTAAAAAAT
*
4399943 AAAATGAAATAAAATAAAATAAAACA
1 AAAATAAAATAAAATAAAATAAAACA
4399969 AAAATAAAATAAAATAAAATAAAA
1 AAAATAAAATAAAATAAAATAAAA
4399993 AATATAATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (26 bp):
AAAATAAAATAAAATAAAATAAAACA
Found at i:4400176 original size:24 final size:24
Alignment explanation
Indices: 4400144--4400219 Score: 125
Period size: 24 Copynumber: 3.2 Consensus size: 24
4400134 GTCTTTGACC
*
4400144 GTTAACTTTAAATCAAACTCCTAA
1 GTTAACTTTAAATCGAACTCCTAA
4400168 GTTAACTTTAAATCGAACTCCTAA
1 GTTAACTTTAAATCGAACTCCTAA
* *
4400192 GTTAACTTTAAATCGAACTTCTGA
1 GTTAACTTTAAATCGAACTCCTAA
4400216 GTTA
1 GTTA
4400220 TCTTCAACTT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (24 bp):
GTTAACTTTAAATCGAACTCCTAA
Found at i:4403385 original size:11 final size:11
Alignment explanation
Indices: 4403369--4403395 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
4403359 CCACTGGATA
4403369 GATCACAGATC
1 GATCACAGATC
4403380 GATCACAGATC
1 GATCACAGATC
4403391 GATCA
1 GATCA
4403396 ACCAACTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.19
Consensus pattern (11 bp):
GATCACAGATC
Found at i:4405530 original size:19 final size:19
Alignment explanation
Indices: 4405501--4405559 Score: 65
Period size: 15 Copynumber: 3.3 Consensus size: 19
4405491 TGAAAATATT
4405501 TAATAAAATAAAATAGATAA
1 TAAT-AAATAAAATAGATAA
4405521 TAATAAATAAAAT-GA-AA
1 TAATAAATAAAATAGATAA
4405538 -AAT-AATAAAATA-ATAAA
1 TAATAAATAAAATAGAT-AA
4405555 TAATA
1 TAATA
4405560 GTAGTAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
15 9 0.26
16 3 0.09
17 4 0.12
18 5 0.15
19 9 0.26
20 4 0.12
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.25
Consensus pattern (19 bp):
TAATAAATAAAATAGATAA
Found at i:4405549 original size:24 final size:23
Alignment explanation
Indices: 4405501--4405554 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
4405491 TGAAAATATT
4405501 TAATAAAATAAAATAGATAATAA
1 TAATAAAATAAAATAGATAATAA
4405524 TAAATAAAATGAAAAATA-ATAA-AA
1 T-AATAAAAT--AAAATAGATAATAA
4405548 TAATAAA
1 TAATAAA
4405555 TAATAGTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 7 0.25
24 11 0.39
25 4 0.14
26 6 0.21
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (23 bp):
TAATAAAATAAAATAGATAATAA
Found at i:4405621 original size:18 final size:18
Alignment explanation
Indices: 4405600--4405642 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
4405590 ATTGTTTTTA
*
4405600 AAATAAAAGTTAAA-AATT
1 AAATAAAAG-AAAATAATT
4405618 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAATAATT
4405636 AAATAAA
1 AAATAAA
4405643 CAAATGAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (18 bp):
AAATAAAAGAAAATAATT
Found at i:4406357 original size:75 final size:76
Alignment explanation
Indices: 4406234--4406383 Score: 225
Period size: 75 Copynumber: 2.0 Consensus size: 76
4406224 TAAAACATCT
* * *
4406234 TAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAA-AAATAT-TAATATTT
1 TAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAAATA-TA
4406297 AAAATAATATTC
65 AAAATAATATTC
*
4406309 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
1 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
4406373 AAAATAATATT
65 AAAATAATATT
4406384 ATCCTAAAAC
Statistics
Matches: 68, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
74 5 0.07
75 42 0.62
76 17 0.25
77 4 0.06
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.31
Consensus pattern (76 bp):
TAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
AAATAATATTC
Found at i:4416220 original size:21 final size:22
Alignment explanation
Indices: 4416195--4416255 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
4416185 AAAACAACCG
4416195 AAAATGTGTCATAAAAG-CATA
1 AAAATGTGTCATAAAAGACATA
* *
4416216 AAAATGTGTTAT-AAAGACATG
1 AAAATGTGTCATAAAAGACATA
*
4416237 AAAACGTGTCAT-AAAGACA
1 AAAATGTGTCATAAAAGACA
4416256 AAATTTTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.11
21 31 0.89
ACGTcount: A:0.51, C:0.10, G:0.16, T:0.23
Consensus pattern (22 bp):
AAAATGTGTCATAAAAGACATA
Found at i:4420232 original size:19 final size:21
Alignment explanation
Indices: 4420204--4420252 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
4420194 ATGTTTCTTA
4420204 TACT-ATTTTA-CATTTT-TG
1 TACTGATTTTATCATTTTATG
4420222 TACTGATTTTATCATTTTATG
1 TACTGATTTTATCATTTTATG
*
4420243 TTCTG-TTTTA
1 TACTGATTTTA
4420253 AGTCATCCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 4 0.15
19 6 0.22
20 11 0.41
21 6 0.22
ACGTcount: A:0.20, C:0.10, G:0.08, T:0.61
Consensus pattern (21 bp):
TACTGATTTTATCATTTTATG
Found at i:4421448 original size:23 final size:23
Alignment explanation
Indices: 4421418--4421466 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
4421408 AGGTCATATG
4421418 CTAGTTGATAGCTGTGTCCTATT
1 CTAGTTGATAGCTGTGTCCTATT
4421441 CTAGTTGATAGCTGTGTCCTATT
1 CTAGTTGATAGCTGTGTCCTATT
4421464 CTA
1 CTA
4421467 TCATGTTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.43
Consensus pattern (23 bp):
CTAGTTGATAGCTGTGTCCTATT
Found at i:4424953 original size:18 final size:18
Alignment explanation
Indices: 4424938--4424984 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
4424928 TCAGTGGTTT
4424938 TTCGAGACAAAGTGGTCA
1 TTCGAGACAAAGTGGTCA
* *
4424956 TTCGGGACATAGTGGTCA
1 TTCGAGACAAAGTGGTCA
4424974 TTCGAGACAAA
1 TTCGAGACAAA
4424985 TATTTAGTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (18 bp):
TTCGAGACAAAGTGGTCA
Found at i:4431620 original size:24 final size:24
Alignment explanation
Indices: 4431593--4431651 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 24
4431583 ATGTGAAATA
4431593 ATGAAAGTGATCA-TATGTGTGCAT
1 ATGAAAGTGAT-ATTATGTGTGCAT
**
4431617 ATG-AAGTGA-ATTATGTGTTTAT
1 ATGAAAGTGATATTATGTGTGCAT
4431639 ATGAAAAGTGATA
1 ATG-AAAGTGATA
4431652 AAAGAGATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
21 1 0.03
22 12 0.41
23 6 0.21
24 9 0.31
25 1 0.03
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (24 bp):
ATGAAAGTGATATTATGTGTGCAT
Found at i:4433675 original size:14 final size:14
Alignment explanation
Indices: 4433656--4433688 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
4433646 GAATATGTAT
4433656 ATGGTTCTTAAGGA
1 ATGGTTCTTAAGGA
4433670 ATGGTTCTTAAGGA
1 ATGGTTCTTAAGGA
*
4433684 GTGGT
1 ATGGT
4433689 CCTTCGGGAC
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:0.24, C:0.06, G:0.33, T:0.36
Consensus pattern (14 bp):
ATGGTTCTTAAGGA
Found at i:4434297 original size:22 final size:21
Alignment explanation
Indices: 4434272--4434313 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4434262 GTAGCAGTAC
*
4434272 TGTAGTAAGGGTATCGGTACCA
1 TGTAG-AAGGGTATCGATACCA
*
4434294 TGTAGCAGGGTATCGATACC
1 TGTAGAAGGGTATCGATACC
4434314 GTATTTGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (21 bp):
TGTAGAAGGGTATCGATACCA
Found at i:4442192 original size:27 final size:27
Alignment explanation
Indices: 4442162--4442221 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
4442152 TCATTCCAAG
4442162 ACTT-AGAGGTATTTTTGGTCATTTTAC
1 ACTTCAGAGGTA-TTTTGGTCATTTTAC
* *
4442189 ACTTCAGGGGTATTTTGGTCATTTTTC
1 ACTTCAGAGGTATTTTGGTCATTTTAC
4442216 ACTTCA
1 ACTTCA
4442222 ATCTAGTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 24 0.80
28 6 0.20
ACGTcount: A:0.20, C:0.15, G:0.18, T:0.47
Consensus pattern (27 bp):
ACTTCAGAGGTATTTTGGTCATTTTAC
Found at i:4442200 original size:28 final size:27
Alignment explanation
Indices: 4442169--4442221 Score: 88
Period size: 27 Copynumber: 1.9 Consensus size: 27
4442159 AAGACTTAGA
4442169 GGTATTTTTGGTCATTTTACACTTCAGG
1 GGTA-TTTTGGTCATTTTACACTTCAGG
*
4442197 GGTATTTTGGTCATTTTTCACTTCA
1 GGTATTTTGGTCATTTTACACTTCA
4442222 ATCTAGTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.17, C:0.15, G:0.19, T:0.49
Consensus pattern (27 bp):
GGTATTTTGGTCATTTTACACTTCAGG
Found at i:4447747 original size:5 final size:5
Alignment explanation
Indices: 4447707--4447737 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
4447697 TGTCCAAATT
4447707 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
4447738 CTTTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:4447934 original size:40 final size:39
Alignment explanation
Indices: 4447809--4448083 Score: 228
Period size: 39 Copynumber: 7.1 Consensus size: 39
4447799 TTTTTGAAAA
*
4447809 ATAG-TTTTG-AAACATTTTGAAAACATATATATATAATAT
1 ATAGTTTTTGAAAATATTTTGAAAAC--ATATATATAATAT
* * * * * * *
4447848 GTAATTTTTTAAAACGATTTTTG-GAA-ATGTATATATTAT
1 ATAGTTTTTGAAAA-TA-TTTTGAAAACATATATATAATAT
*
4447887 ATAGTTTTTGAAAAATATTTTGAAAACGTATATATAATAT
1 ATAGTTTTTG-AAAATATTTTGAAAACATATATATAATAT
* *
4447927 ATGGTTTTT-AAAATATTTTGAAAACATTTATATAATAT
1 ATAGTTTTTGAAAATATTTTGAAAACATATATATAATAT
*
4447965 ATAGTTTTTGAAAATATTTTTAAAA-ATATATAT-AT-T
1 ATAGTTTTTGAAAATATTTTGAAAACATATATATAATAT
* ** * *
4448001 ATAG-TTTTGAAAATAAATTCCAAAAAATATATATTATAT
1 ATAGTTTTTGAAAAT-ATTTTGAAAACATATATATAATAT
* *
4448040 ATAG-TTTTGAAAATTATTTTTAAATATATATATATATATAT
1 ATAGTTTTTGAAAA-TATTTTGAAA-ACATATATATA-ATAT
4448081 ATA
1 ATA
4448084 TATATATTAT
Statistics
Matches: 192, Mismatches: 29, Indels: 28
0.77 0.12 0.11
Matches are distributed among these distances:
35 10 0.05
36 12 0.06
37 10 0.05
38 49 0.26
39 57 0.30
40 36 0.19
41 10 0.05
42 3 0.02
43 5 0.03
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (39 bp):
ATAGTTTTTGAAAATATTTTGAAAACATATATATAATAT
Found at i:4448070 original size:2 final size:2
Alignment explanation
Indices: 4448063--4448096 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
4448053 TTATTTTTAA
4448063 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4448097 GATTTGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4448088 original size:54 final size:53
Alignment explanation
Indices: 4448027--4448139 Score: 187
Period size: 54 Copynumber: 2.2 Consensus size: 53
4448017 ATTCCAAAAA
*
4448027 ATATATAT-TA-TATATAGTTTTGAAAATTATTTTTAAATATATATATATATAT
1 ATATATATATATTATATAGATTTGAAAATTATTTTTAAA-ATATATATATATAT
4448079 ATATATATATATTATATAGATTTGAAAATTATTTTTAAAATATATATATATAT
1 ATATATATATATTATATAGATTTGAAAATTATTTTTAAAATATATATATATAT
4448132 AT-TATATA
1 ATATATATA
4448140 GTTTTGAAAA
Statistics
Matches: 58, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
52 14 0.24
53 18 0.31
54 26 0.45
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (53 bp):
ATATATATATATTATATAGATTTGAAAATTATTTTTAAAATATATATATATAT
Found at i:4448122 original size:43 final size:43
Alignment explanation
Indices: 4447877--4448237 Score: 201
Period size: 38 Copynumber: 8.8 Consensus size: 43
4447867 TTTGGAAATG
* * **
4447877 TATATATTATATAGTTTTTGAAAAATA-TTTTGAAA-ACGTATA
1 TATATATTATATAG-TTTTGAAAATTATTTTTAAAATATATATA
* * * *
4447919 TATA-A-TATATGGTTTTTAAAA-TATTTTGAAAACAT-T-TA
1 TATATATTATATAGTTTTGAAAATTATTTTTAAAATATATATA
4447957 TATA-A-TATATAGTTTTTGAAAA-TATTTTT--AA-A-A-ATA
1 TATATATTATATAG-TTTTGAAAATTATTTTTAAAATATATATA
* * **
4447993 TATATA-T-TATAGTTTTGAAAATAAATTCCAAAA-A-ATATA
1 TATATATTATATAGTTTTGAAAATTATTTTTAAAATATATATA
4448032 TAT-TA-TATATAGTTTTGAAAATTATTTTTAAATATATATATATATATATATA
1 TATATATTATATAGTTTTGAAAATTA---TT---T-T-TA-A-A-ATATATATA
*
4448084 TATATATTATATAGATTTGAAAATTATTTTTAAAATATATATA
1 TATATATTATATAGTTTTGAAAATTATTTTTAAAATATATATA
* *
4448127 TATATATTATATAGTTTTGAAAATTAATTTT--AA-A-ACA-A
1 TATATATTATATAGTTTTGAAAATTATTTTTAAAATATATATA
* *
4448165 TATATATTATATAGTTTTGAAAATCATTTTTGAAAA-ACATATA
1 TATATATTATATAGTTTTGAAAATTATTTTT-AAAATATATATA
* *
4448208 TAT-TA-TATA-A-TTTT-AAAAATGTTTTTAAAA
1 TATATATTATATAGTTTTGAAAATTATTTTTAAAA
4448238 ACATATTTCA
Statistics
Matches: 262, Mismatches: 26, Indels: 67
0.74 0.07 0.19
Matches are distributed among these distances:
35 9 0.03
36 15 0.06
37 8 0.03
38 61 0.23
39 57 0.22
40 9 0.03
41 10 0.04
42 9 0.03
43 42 0.16
44 1 0.00
45 2 0.01
46 2 0.01
47 2 0.01
48 2 0.01
49 1 0.00
50 1 0.00
51 3 0.01
52 8 0.03
53 2 0.01
54 18 0.07
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.47
Consensus pattern (43 bp):
TATATATTATATAGTTTTGAAAATTATTTTTAAAATATATATA
Found at i:4448257 original size:81 final size:80
Alignment explanation
Indices: 4448083--4448237 Score: 205
Period size: 81 Copynumber: 2.0 Consensus size: 80
4448073 ATATATATAT
* * *
4448083 ATATATATTATATAGATTTGAAAATTATTTTTAAAATATATATATATATATTATATAGTTTTGAA
1 ATATATATTATATAGATTTGAAAATCATTTTTAAAATACATATATATATATTATATAGTTTTAAA
4448148 AATTAATTTTAAAACA
66 AATT-ATTTTAAAACA
*
4448164 ATATATATTATATAGTTTTGAAAATCATTTTTGAAAA-ACATATATAT-TA-TATA-A-TTTTAA
1 ATATATATTATATAGATTTGAAAATCATTTTT-AAAATACATATATATATATTATATAGTTTTAA
4448224 AAATGT-TTTTAAAA
65 AAAT-TATTTTAAAA
4448238 ACATATTTCA
Statistics
Matches: 68, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
76 8 0.12
77 9 0.13
78 2 0.03
79 4 0.06
80 2 0.03
81 39 0.57
82 4 0.06
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (80 bp):
ATATATATTATATAGATTTGAAAATCATTTTTAAAATACATATATATATATTATATAGTTTTAAA
AATTATTTTAAAACA
Found at i:4449719 original size:22 final size:20
Alignment explanation
Indices: 4449634--4449724 Score: 73
Period size: 21 Copynumber: 4.5 Consensus size: 20
4449624 AAATTTACCC
*
4449634 TTTATTAGTA-TTTTTT-AT
1 TTTATTATTATTTTTTTAAT
* *
4449652 TTTATT-TTATTTTCCCTTATT
1 TTTATTATTATTTT--TTTAAT
4449673 TTTATTATTATTTTTTTAAT
1 TTTATTATTATTTTTTTAAT
4449693 CTTTATTCATCTATTTTATTT-AT
1 -TTTATT-AT-TATTTT-TTTAAT
4449716 TTTATTATT
1 TTTATTATT
4449725 TTTCTTATAT
Statistics
Matches: 59, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
17 2 0.03
18 9 0.15
20 7 0.12
21 15 0.25
22 15 0.25
23 8 0.14
24 3 0.05
ACGTcount: A:0.21, C:0.07, G:0.01, T:0.71
Consensus pattern (20 bp):
TTTATTATTATTTTTTTAAT
Found at i:4449760 original size:26 final size:23
Alignment explanation
Indices: 4449715--4449773 Score: 57
Period size: 26 Copynumber: 2.4 Consensus size: 23
4449705 ATTTTATTTA
*
4449715 TTTTATTATTTTTCTTATATTAGTAT
1 TTTTATT-TTTTTCTTATA-T-CTAT
4449741 TTTTATTTTGTTT-TTCATATCTAT
1 TTTTATTTT-TTTCTT-ATATCTAT
4449765 TTTTATTTT
1 TTTTATTTT
4449774 ACAATCTAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
24 12 0.40
25 5 0.17
26 13 0.43
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.73
Consensus pattern (23 bp):
TTTTATTTTTTTCTTATATCTAT
Found at i:4459453 original size:13 final size:14
Alignment explanation
Indices: 4459435--4459464 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
4459425 TAAGGGGGAG
4459435 TAATTTCAAAA-CT
1 TAATTTCAAAATCT
4459448 TAATTTCAAAATCT
1 TAATTTCAAAATCT
4459462 TAA
1 TAA
4459465 AATTACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (14 bp):
TAATTTCAAAATCT
Found at i:4471916 original size:85 final size:85
Alignment explanation
Indices: 4471773--4472022 Score: 356
Period size: 85 Copynumber: 2.9 Consensus size: 85
4471763 TCCCAGCTTA
* * *
4471773 TTACAATATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTT
1 TTACAGTATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTC
4471838 AGCTCAAAGACATACCAAAT
66 AGCTCAAAGACATACCAAAT
*
4471858 TTACAGTATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAATACCTTCGAGTTCGATTACATTC
1 TTACAGTATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTC
4471923 AGCTCAAAGACATACCAAAT
66 AGCTCAAAGACATACCAAAT
* * * * * ** * *
4471943 TTACAGCATAACTCAAGACGATAAGGGCTATCTGTCAACAAAAAAATATCGAGTTTGATTCCATT
1 TTACAGTATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCT-TCGAGTTCGATTACATT
* *
4472008 CAGCTCGATGACATA
65 CAGCTCAAAGACATA
4472023 TCAATCGCAT
Statistics
Matches: 149, Mismatches: 15, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
85 121 0.81
86 28 0.19
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (85 bp):
TTACAGTATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTC
AGCTCAAAGACATACCAAAT
Found at i:4472924 original size:38 final size:38
Alignment explanation
Indices: 4472877--4472973 Score: 103
Period size: 36 Copynumber: 2.6 Consensus size: 38
4472867 TTGAAAAAAC
* *
4472877 ATATAATATA-CTTTTTAAAAATCAGTTTT-CAAA-A-AT
1 ATATAATATATATTTTTAAAAAT-A-TTTTAAAAACATAT
* *
4472913 ATATAATATATAGTTTTGAAAATATTTTAAAAACATAT
1 ATATAATATATATTTTTAAAAATATTTTAAAAACATAT
4472951 ATATAATATATAGTTTTTAAAAA
1 ATATAATATATA-TTTTTAAAAA
4472974 CGGTTTTTGG
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
35 4 0.08
36 14 0.28
37 10 0.20
38 14 0.28
39 8 0.16
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (38 bp):
ATATAATATATATTTTTAAAAATATTTTAAAAACATAT
Found at i:4473017 original size:26 final size:26
Alignment explanation
Indices: 4472976--4473027 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
4472966 TTTAAAAACG
* * *
4472976 GTTTTTGGAAATGTATATATTATATA
1 GTTTTTGAAAACGTATATATAATATA
4473002 GTTTTTGAAAACGTATATATAATATA
1 GTTTTTGAAAACGTATATATAATATA
4473028 TGGTTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.46
Consensus pattern (26 bp):
GTTTTTGAAAACGTATATATAATATA
Found at i:4473021 original size:67 final size:66
Alignment explanation
Indices: 4472937--4473078 Score: 173
Period size: 66 Copynumber: 2.1 Consensus size: 66
4472927 TTTGAAAATA
* * * *
4472937 TTTTAAAAACATATATATAATATATAGTTTTTAAAAACGGT-TTTTG-GAA-ATGTATATATTAT
1 TTTTGAAAACATATATATAATATAT-GGTTTTAAAAA---TATTTTGAAAATATGTATATAATAT
4472999 ATAGT
62 ATAGT
* *
4473004 TTTTGAAAACGTATATATAATATATGGTTTTAAAAATATTTTGAAAATATTTATATAATATATAG
1 TTTTGAAAACATATATATAATATATGGTTTTAAAAATATTTTGAAAATATGTATATAATATATAG
4473069 T
66 T
4473070 TTTTGAAAA
1 TTTTGAAAA
4473079 TATTTTTGAA
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
63 1 0.02
64 5 0.08
65 2 0.03
66 35 0.53
67 23 0.35
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (66 bp):
TTTTGAAAACATATATATAATATATGGTTTTAAAAATATTTTGAAAATATGTATATAATATATAG
T
Found at i:4473033 original size:28 final size:26
Alignment explanation
Indices: 4472975--4473034 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 26
4472965 TTTTAAAAAC
* *
4472975 GGTTTTTGGAAATGTATATATTATAT
1 GGTTTTTGAAAACGTATATATTATAT
*
4473001 AGTTTTTGAAAACGTATATATAATATAT
1 GGTTTTTGAAAACGTATATAT--TATAT
4473029 GGTTTT
1 GGTTTT
4473035 AAAAATATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 18 0.64
28 10 0.36
ACGTcount: A:0.33, C:0.02, G:0.17, T:0.48
Consensus pattern (26 bp):
GGTTTTTGAAAACGTATATATTATAT
Found at i:4473086 original size:40 final size:40
Alignment explanation
Indices: 4473003--4473108 Score: 135
Period size: 38 Copynumber: 2.7 Consensus size: 40
4472993 TATTATATAG
**
4473003 TTTTTGAAAACGTATATATAATATAT-GGTTTTAAAAATA
1 TTTTTGAAAATATATATATAATATATAGGTTTTAAAAATA
* * *
4473042 -TTTTGAAAATATTTATATAATATATAGTTTTTGAAAATA
1 TTTTTGAAAATATATATATAATATATAGGTTTTAAAAATA
*
4473081 TTTTTGAATATATATATATATATATATA
1 TTTTTGAAAATATATATATA-ATATATA
4473109 TATATATATA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
38 22 0.39
39 11 0.19
40 17 0.30
41 7 0.12
ACGTcount: A:0.43, C:0.01, G:0.08, T:0.48
Consensus pattern (40 bp):
TTTTTGAAAATATATATATAATATATAGGTTTTAAAAATA
Found at i:4473095 original size:2 final size:2
Alignment explanation
Indices: 4473088--4473125 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
4473078 ATATTTTTGA
4473088 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4473126 GTTTTGAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4473105 original size:105 final size:105
Alignment explanation
Indices: 4472911--4473106 Score: 279
Period size: 105 Copynumber: 1.9 Consensus size: 105
4472901 GTTTTCAAAA
*
4472911 ATATATAATATATAGTTTTGAAAATATTTTAAAAACATATATATAATATATAGTTTTTAAAAACG
1 ATATATAATATATAGTTTTAAAAATATTTTAAAAACATATATATAATATATAGTTTTTAAAAACG
* *
4472976 GTTTTTGGAAATGTATATATTATATAGTTTTTGAAAACGT
66 ATTTTTGGAAATATATATATTATATAGTTTTTGAAAACGT
* * * * * *
4473016 ATATATAATATATGGTTTTAAAAATATTTTGAAAATATTTATATAATATATAGTTTTTGAAAA-T
1 ATATATAATATATAGTTTTAAAAATATTTTAAAAACATATATATAATATATAGTTTTTAAAAACG
4473080 ATTTTT-GAATATATATATATATATATA
66 ATTTTTGGAA-ATATATATAT-TATATA
4473107 TATATATATA
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
103 3 0.04
104 14 0.17
105 63 0.79
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.46
Consensus pattern (105 bp):
ATATATAATATATAGTTTTAAAAATATTTTAAAAACATATATATAATATATAGTTTTTAAAAACG
ATTTTTGGAAATATATATATTATATAGTTTTTGAAAACGT
Found at i:4473505 original size:45 final size:44
Alignment explanation
Indices: 4473439--4473530 Score: 157
Period size: 45 Copynumber: 2.1 Consensus size: 44
4473429 GGCAACATCT
*
4473439 GTCCCCATCTCTGGCGAAATCCATCCCCATCTCCGGCGAAATCC
1 GTCCCCATCTCTGGCAAAATCCATCCCCATCTCCGGCGAAATCC
*
4473483 GTCCCCATCTCCTGGCAAAATCCATCCCCATCTCCTGCGAAATCC
1 GTCCCCATCT-CTGGCAAAATCCATCCCCATCTCCGGCGAAATCC
4473528 GTC
1 GTC
4473531 TATCTCCATC
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 10 0.22
45 35 0.78
ACGTcount: A:0.21, C:0.43, G:0.14, T:0.22
Consensus pattern (44 bp):
GTCCCCATCTCTGGCAAAATCCATCCCCATCTCCGGCGAAATCC
Found at i:4473510 original size:23 final size:23
Alignment explanation
Indices: 4473440--4473527 Score: 137
Period size: 22 Copynumber: 4.0 Consensus size: 23
4473430 GCAACATCTG
4473440 TCCCCATCT-CTGGCGAAATCCA
1 TCCCCATCTCCTGGCGAAATCCA
*
4473462 TCCCCATCTCC-GGCGAAATCCG
1 TCCCCATCTCCTGGCGAAATCCA
*
4473484 TCCCCATCTCCTGGCAAAATCCA
1 TCCCCATCTCCTGGCGAAATCCA
4473507 TCCCCATCTCCT-GCGAAATCC
1 TCCCCATCTCCTGGCGAAATCC
4473528 GTCTATCTCC
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
22 38 0.63
23 22 0.37
ACGTcount: A:0.22, C:0.44, G:0.12, T:0.22
Consensus pattern (23 bp):
TCCCCATCTCCTGGCGAAATCCA
Found at i:4473892 original size:20 final size:20
Alignment explanation
Indices: 4473869--4473907 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
4473859 TTTGAAACTT
4473869 AAATTCGCAACACGAAAATG
1 AAATTCGCAACACGAAAATG
4473889 AAATTCGCAACACGAAAAT
1 AAATTCGCAACACGAAAAT
4473908 CGCAACGCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.21, G:0.13, T:0.15
Consensus pattern (20 bp):
AAATTCGCAACACGAAAATG
Found at i:4475336 original size:42 final size:42
Alignment explanation
Indices: 4475277--4475368 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
4475267 CTTCGAGTGT
* * *
4475277 CATCACCTGATCGAGCCGATTCTACAGCTCGACACCCAGAGC
1 CATCACCTGATCGAGCCGATTATACACCTCGACAACCAGAGC
* * *
4475319 CATCACTTGATCGAGCCGATTATACACCTCTACAACGAGAGC
1 CATCACCTGATCGAGCCGATTATACACCTCGACAACCAGAGC
4475361 CATCACCT
1 CATCACCT
4475369 ATTCCATTAC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.28, C:0.36, G:0.16, T:0.20
Consensus pattern (42 bp):
CATCACCTGATCGAGCCGATTATACACCTCGACAACCAGAGC
Found at i:4475762 original size:4 final size:4
Alignment explanation
Indices: 4475753--4475798 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
4475743 TTTTTCGGCA
* * * *
4475753 TTAT TTAT TTAT TTAT TTAT TTAC TGAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
4475799 TTAGTGGCCC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.67
Consensus pattern (4 bp):
TTAT
Found at i:4475974 original size:21 final size:21
Alignment explanation
Indices: 4475948--4476039 Score: 96
Period size: 21 Copynumber: 4.4 Consensus size: 21
4475938 CCTATCATCA
* * *
4475948 TTCAAGAGGCCCCTCCTATCG
1 TTCAAGAGGCCCATCCCACCG
*
4475969 TTCAAGAGGCCCATCCCACCA
1 TTCAAGAGGCCCATCCCACCG
* ** *
4475990 TTCAAGAGGCTCATGTCATCG
1 TTCAAGAGGCCCATCCCACCG
4476011 TTCAAGAGGTCCC-TCCCACCG
1 TTCAAGAGG-CCCATCCCACCG
4476032 TTCAAGAG
1 TTCAAGAG
4476040 CCTGATTCAC
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
21 55 0.96
22 2 0.04
ACGTcount: A:0.24, C:0.35, G:0.20, T:0.22
Consensus pattern (21 bp):
TTCAAGAGGCCCATCCCACCG
Found at i:4475993 original size:42 final size:42
Alignment explanation
Indices: 4475946--4476039 Score: 120
Period size: 42 Copynumber: 2.2 Consensus size: 42
4475936 CACCTATCAT
*
4475946 CATTCAAGAGGCCCCTC-CTATCGTTCAAGAGG-CCCATCCCAC
1 CATTCAAGAGGCCCATCTC-ATCGTTCAAGAGGTCCC-TCCCAC
* *
4475988 CATTCAAGAGGCTCATGTCATCGTTCAAGAGGTCCCTCCCAC
1 CATTCAAGAGGCCCATCTCATCGTTCAAGAGGTCCCTCCCAC
*
4476030 CGTTCAAGAG
1 CATTCAAGAG
4476040 CCTGATTCAC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 42 0.91
43 4 0.09
ACGTcount: A:0.24, C:0.35, G:0.19, T:0.21
Consensus pattern (42 bp):
CATTCAAGAGGCCCATCTCATCGTTCAAGAGGTCCCTCCCAC
Found at i:4479856 original size:24 final size:23
Alignment explanation
Indices: 4479819--4479863 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
4479809 CCGTGGCATT
4479819 TTCTTTTTTTTTCTTC-GGGTAC
1 TTCTTTTTTTTTCTTCAGGGTAC
4479841 TTCTTCTTTTTCTTCTTCAGGGT
1 TTCTT-TTTTT-TTCTTCAGGGT
4479864 TATATGAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 5 0.25
23 5 0.25
24 6 0.30
25 4 0.20
ACGTcount: A:0.04, C:0.20, G:0.13, T:0.62
Consensus pattern (23 bp):
TTCTTTTTTTTTCTTCAGGGTAC
Found at i:4480067 original size:24 final size:24
Alignment explanation
Indices: 4480033--4480082 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
4480023 CTGAAACATC
4480033 ATCAAAATCCGAGTATCGACCAAG
1 ATCAAAATCCGAGTATCGACCAAG
* * *
4480057 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATCGACCAAG
4480081 AT
1 AT
4480083 TAAATTTCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATCGACCAAG
Found at i:4480232 original size:12 final size:12
Alignment explanation
Indices: 4480211--4480244 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
4480201 GGTTGTCGGT
*
4480211 TTTGAAATTGTG
1 TTTGATATTGTG
4480223 TTTGATATTGTG
1 TTTGATATTGTG
*
4480235 TTTGGTATTG
1 TTTGATATTG
4480245 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.18, C:0.00, G:0.26, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:4481056 original size:20 final size:21
Alignment explanation
Indices: 4481031--4481185 Score: 78
Period size: 20 Copynumber: 7.6 Consensus size: 21
4481021 AAATAAAACT
4481031 TGTTGCGAAATT-AAAATTCG
1 TGTTGCGAAATTGAAAATTCG
4481051 TGTTGCG-AATTCGAAAA-TCG
1 TGTTGCGAAATT-GAAAATTCG
* *** *
4481071 AGTTGC-AAAAACAAAATTCA
1 TGTTGCGAAATTGAAAATTCG
* *
4481091 CGTTGCG-AATTCAGAAA-TCG
1 TGTTGCGAAATTGA-AAATTCG
*
4481111 AGTTGC-AAATTTG-AAATTCAG
1 TGTTGCGAAA-TTGAAAATTC-G
* *
4481132 TGTTGCGAATTTGGGAAA-TCG
1 TGTTGCGAAATT-GAAAATTCG
* * *
4481153 CGTTGCGAATTTGGAAATT-G
1 TGTTGCGAAATTGAAAATTCG
4481173 TGTTGCGAAATTG
1 TGTTGCGAAATTG
4481186 GAGTTTGCGT
Statistics
Matches: 105, Mismatches: 16, Indels: 28
0.70 0.11 0.19
Matches are distributed among these distances:
19 11 0.10
20 56 0.53
21 30 0.29
22 5 0.05
23 3 0.03
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (21 bp):
TGTTGCGAAATTGAAAATTCG
Found at i:4481087 original size:40 final size:40
Alignment explanation
Indices: 4481043--4481142 Score: 121
Period size: 40 Copynumber: 2.5 Consensus size: 40
4481033 TTGCGAAATT
4481043 AAAATTCGTGTTGCGAATTC-GAAAATCGAGTTGCAAAAAC
1 AAAATTCGTGTTGCGAATTCAG-AAATCGAGTTGCAAAAAC
** ***
4481083 AAAATTCACGTTGCGAATTCAGAAATCGAGTTGCAAATTT
1 AAAATTCGTGTTGCGAATTCAGAAATCGAGTTGCAAAAAC
*
4481123 GAAATTCAGTGTTGCGAATT
1 AAAATTC-GTGTTGCGAATT
4481143 TGGGAAATCG
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
40 39 0.78
41 11 0.22
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (40 bp):
AAAATTCGTGTTGCGAATTCAGAAATCGAGTTGCAAAAAC
Found at i:4481157 original size:21 final size:20
Alignment explanation
Indices: 4481091--4481203 Score: 93
Period size: 20 Copynumber: 5.5 Consensus size: 20
4481081 ACAAAATTCA
**
4481091 CGTTGCGAATTCAGAAATCG
1 CGTTGCGAATTTGGAAATCG
* *
4481111 AGTTGCAAATTT-GAAATTCAG
1 CGTTGCGAATTTGGAAA-TC-G
*
4481132 TGTTGCGAATTTGGGAAATCG
1 CGTTGCGAATTT-GGAAATCG
*
4481153 CGTTGCGAATTTGGAAATTG
1 CGTTGCGAATTTGGAAATCG
* * ** *
4481173 TGTTGCGAAATTGGAGTTTG
1 CGTTGCGAATTTGGAAATCG
4481193 CGTTGCGAATT
1 CGTTGCGAATT
4481204 CGAGATCGAG
Statistics
Matches: 76, Mismatches: 13, Indels: 8
0.78 0.13 0.08
Matches are distributed among these distances:
19 4 0.05
20 43 0.57
21 23 0.30
22 2 0.03
23 4 0.05
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.34
Consensus pattern (20 bp):
CGTTGCGAATTTGGAAATCG
Found at i:4481164 original size:42 final size:40
Alignment explanation
Indices: 4481104--4481203 Score: 112
Period size: 42 Copynumber: 2.5 Consensus size: 40
4481094 TGCGAATTCA
* * *
4481104 GAAATCGAGTTGCAAATTT-GAAATTCAGTGTTGCGAATTTGG
1 GAAATCGCGTTGCGAATTTGGAAATT--GTGTTGCGAAATT-G
4481146 GAAATCGCGTTGCGAATTTGGAAATTGTGTTGCGAAATTG
1 GAAATCGCGTTGCGAATTTGGAAATTGTGTTGCGAAATTG
** *
4481186 GAGTTTGCGTTGCGAATT
1 GAAATCGCGTTGCGAATT
4481204 CGAGATCGAG
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
40 16 0.31
41 12 0.24
42 17 0.33
43 6 0.12
ACGTcount: A:0.27, C:0.10, G:0.29, T:0.34
Consensus pattern (40 bp):
GAAATCGCGTTGCGAATTTGGAAATTGTGTTGCGAAATTG
Found at i:4481385 original size:38 final size:38
Alignment explanation
Indices: 4481310--4481525 Score: 299
Period size: 38 Copynumber: 5.5 Consensus size: 38
4481300 TTTCTCTTTC
*
4481310 AAAAATATATATATTATATATATTTTTTGAAAATTATTTTT
1 AAAAATATATATA-T-TATATA-GTTTTGAAAATTATTTTT
*
4481351 AAAAATATATATATTATATTGTTTTGAAAATTATTTTT
1 AAAAATATATATATTATATAGTTTTGAAAATTATTTTT
*
4481389 ACAAATTATATATATATTATATAGTTTTAAAAATTATTTTT
1 A-AAA--ATATATATATTATATAGTTTTGAAAATTATTTTT
*
4481430 AAATATATATATATTATATAGTTTTGAAAATTATTTTT
1 AAAAATATATATATTATATAGTTTTGAAAATTATTTTT
*
4481468 AAAACA-ATATATATTATATAGTTTTGAAAATCATTTTT
1 AAAA-ATATATATATTATATAGTTTTGAAAATTATTTTT
*
4481506 GAAAAACATATATATTATAT
1 -AAAAATATATATATTATAT
4481526 GATTTTAAAA
Statistics
Matches: 161, Mismatches: 8, Indels: 14
0.88 0.04 0.08
Matches are distributed among these distances:
38 86 0.53
39 26 0.16
40 3 0.02
41 46 0.29
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (38 bp):
AAAAATATATATATTATATAGTTTTGAAAATTATTTTT
Found at i:4481438 original size:79 final size:77
Alignment explanation
Indices: 4481310--4481525 Score: 301
Period size: 79 Copynumber: 2.8 Consensus size: 77
4481300 TTTCTCTTTC
* *
4481310 AAAA-ATATATATATTATATATATTTTTTGAAAATTATTTTTAAAAATATATATATTATATTGTT
1 AAAACATATATATA-T-TATATA-GTTTTGAAAATTATTTTTAAAAATATATATATTATATAGTT
4481374 TTGAAAATTATTTTT
63 TTGAAAATTATTTTT
* * *
4481389 ACAAATTATATATATATTATATAGTTTTAAAAATTATTTTTAAATATATATATATTATATAGTTT
1 A-AAA-CATATATATATTATATAGTTTTGAAAATTATTTTTAAAAATATATATATTATATAGTTT
4481454 TGAAAATTATTTTT
64 TGAAAATTATTTTT
* *
4481468 AAAACA-ATATATATTATATAGTTTTGAAAATCATTTTTGAAAAACATATATATTATAT
1 AAAACATATATATATTATATAGTTTTGAAAATTATTTTT-AAAAATATATATATTATAT
4481526 GATTTTAAAA
Statistics
Matches: 124, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
76 30 0.24
77 18 0.15
78 3 0.02
79 54 0.44
80 9 0.07
81 1 0.01
82 9 0.07
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (77 bp):
AAAACATATATATATTATATAGTTTTGAAAATTATTTTTAAAAATATATATATTATATAGTTTTG
AAAATTATTTTT
Found at i:4481554 original size:38 final size:37
Alignment explanation
Indices: 4481311--4481554 Score: 231
Period size: 38 Copynumber: 6.2 Consensus size: 37
4481301 TTCTCTTTCA
* * *
4481311 AAAATATATATATTATATATATTTTTTGAAAATTATTTTT
1 AAAACATATATA-T-TATATA-GTTTTAAAAATTATTTTT
* * *
4481351 AAAAATATATATATTATATTGTTTTGAAAATTATTTTT
1 -AAAACATATATATTATATAGTTTTAAAAATTATTTTT
*
4481389 ACAAATTATATATATATTATATAGTTTTAAAAATTATTTTT
1 --AAA--ACATATATATTATATAGTTTTAAAAATTATTTTT
* *
4481430 AAATATATATATATTATATAGTTTTGAAAATTATTTTT
1 AAA-ACATATATATTATATAGTTTTAAAAATTATTTTT
* *
4481468 AAAACAATATATATTATATAGTTTTGAAAATCATTTTT
1 AAAAC-ATATATATTATATAGTTTTAAAAATTATTTTT
4481506 GAAAAACATATATATTATAT-GATTTTAAAAATGT-TTTTT
1 --AAAACATATATATTATATAG-TTTTAAAAAT-TATTTTT
*
4481545 GAAATCATAT
1 -AAAACATAT
4481555 TTCATTTATT
Statistics
Matches: 183, Mismatches: 12, Indels: 19
0.86 0.06 0.09
Matches are distributed among these distances:
37 1 0.01
38 94 0.51
39 38 0.21
40 6 0.03
41 44 0.24
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (37 bp):
AAAACATATATATTATATAGTTTTAAAAATTATTTTT
Found at i:4482658 original size:26 final size:26
Alignment explanation
Indices: 4482627--4482676 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
4482617 GCATGGTCTT
*
4482627 GTGCATCGATGCATCAAATGCATTTA
1 GTGCATCGATGCATAAAATGCATTTA
4482653 GTGCATCGATGCATAAAATGCATT
1 GTGCATCGATGCATAAAATGCATT
4482677 CGATGTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (26 bp):
GTGCATCGATGCATAAAATGCATTTA
Found at i:4482719 original size:20 final size:20
Alignment explanation
Indices: 4482694--4482731 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4482684 TTGAAAATTA
4482694 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
4482714 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
4482732 CACTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:4484269 original size:3 final size:3
Alignment explanation
Indices: 4484261--4484348 Score: 122
Period size: 3 Copynumber: 29.0 Consensus size: 3
4484251 TTCATTTTAA
**
4484261 ATT ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
4484309 ATT ATT ATT ATT ATT ATT AAT AGT AAT ATT ATTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT
4484349 TAAATATTAC
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
3 73 0.96
4 3 0.04
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:4485175 original size:13 final size:13
Alignment explanation
Indices: 4485157--4485185 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
4485147 ACCACCGTTA
4485157 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
4485170 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
4485183 CGG
1 CGG
4485186 AATACGGTGG
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:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:4485864 original size:54 final size:52
Alignment explanation
Indices: 4485763--4485866 Score: 122
Period size: 52 Copynumber: 2.0 Consensus size: 52
4485753 ATAATTTTAC
* * * *
4485763 ATTTATTATTATTTTATTTATTTATAGTCATTGTTTAGTTATTTTTTACTTA
1 ATTTATTATTATTTTATATATTTATAATCATTCTTTAATTATTTTTTACTTA
4485815 ATTT-TTATTATTTTAATATATTT-TAAATCATTACTTTAATTATTGTTTTACT
1 ATTTATTATTATTTT-ATATATTTAT-AATCATT-CTTTAATTATT-TTTTACT
4485867 ATATTATAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
51 11 0.25
52 17 0.39
53 9 0.20
54 7 0.16
ACGTcount: A:0.28, C:0.05, G:0.04, T:0.63
Consensus pattern (52 bp):
ATTTATTATTATTTTATATATTTATAATCATTCTTTAATTATTTTTTACTTA
Found at i:4485893 original size:35 final size:35
Alignment explanation
Indices: 4485818--4485893 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 35
4485808 TTACTTAATT
*
4485818 TTTATTATTTTAATATATTTTAAATCATTACTTTA
1 TTTATTATTTTAATATATTATAAATCATTACTTTA
* * *
4485853 ATTATTGTTTTACTATATTATAAAT-ATATA-TATTA
1 TTTATTATTTTAATATATTATAAATCAT-TACT-TTA
4485888 TTTATT
1 TTTATT
4485894 TAATAATGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
34 3 0.09
35 31 0.91
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (35 bp):
TTTATTATTTTAATATATTATAAATCATTACTTTA
Found at i:4491261 original size:13 final size:11
Alignment explanation
Indices: 4491230--4491255 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4491220 CTCATCCAAC
4491230 AAAGAAAAAAA
1 AAAGAAAAAAA
4491241 AAAGAAAAAAA
1 AAAGAAAAAAA
4491252 AAAG
1 AAAG
4491256 GGAAAATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:4493539 original size:93 final size:93
Alignment explanation
Indices: 4493354--4493543 Score: 287
Period size: 93 Copynumber: 2.0 Consensus size: 93
4493344 AGAAGACTCA
4493354 ATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATATGGTTTGGTATGAAACCACAGAATCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATATGGTTTGGTATGAAACCACAGAATCAA
* *
4493419 TCATTGAATTTGGAAGATGGATGTGCTC
66 TCATTGAATTTGAAAGATGAATGTGCTC
*
4493447 ATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATATGGTTTGGTATG-AACTCTA-A-AGTC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATATGGTTTGGTATGAAAC-C-ACAGAATC
* *
4493509 AATCATTGGATTTGAAAGATGAATTTTGCTC
64 AATCATTGAATTTGAAAGATGAA-TGTGCTC
4493540 ATAG
1 ATAG
4493544 TAGAAATAAG
Statistics
Matches: 89, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
92 26 0.29
93 62 0.70
94 1 0.01
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (93 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATATGGTTTGGTATGAAACCACAGAATCAA
TCATTGAATTTGAAAGATGAATGTGCTC
Found at i:4494855 original size:75 final size:75
Alignment explanation
Indices: 4494699--4494869 Score: 202
Period size: 75 Copynumber: 2.3 Consensus size: 75
4494689 GAAGCAAATA
* * *
4494699 TTGGGGCATGCTGAAAACCCTTTTCAAACAGAATCAGAAATGTTGAAATATTCTGAATATTTATC
1 TTGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAACATTTATC
4494764 AGCAAAATGC
66 AGCAAAATGC
* * * ** *
4494774 TGGGGGCATGCTGAAAACCCATTTCAATCAGAATCAGAACTGTTGATGCATTTTGAACACTTGTA
1 TTGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAACA-TT-TA
* *
4494839 TTAGC-CAATG-
64 TCAGCAAAATGC
*
4494849 TTGGGGCATGCTGAAGACCCA
1 TTGGGGCATGCTGAAAACCCA
4494870 CAATATCCGG
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
75 69 0.85
76 6 0.07
77 6 0.07
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (75 bp):
TTGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAACATTTATC
AGCAAAATGC
Found at i:4496134 original size:22 final size:22
Alignment explanation
Indices: 4496105--4496159 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
4496095 ATCTACACTC
*
4496105 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
*
4496127 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
4496149 TTCAAAGATGA
1 TTCAAAGATGA
4496160 AAACTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:4497145 original size:77 final size:76
Alignment explanation
Indices: 4496834--4497627 Score: 1455
Period size: 76 Copynumber: 10.4 Consensus size: 76
4496824 CTATTTCTCA
4496834 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
4496899 AGCCTTCGGGT
66 AGCCTTCGGGT
*
4496910 CATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATG-TTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
4496974 AAGCCTTCGGGT
65 AAGCCTTCGGGT
*
4496986 CATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
4497051 AGCCTTCGGGT
66 AGCCTTCGGGT
4497062 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
4497127 AAGCCTTCGGGT
65 AAGCCTTCGGGT
*
4497139 CATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
4497204 AGCCTTCGGGT
66 AGCCTTCGGGT
4497215 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
4497280 AAGCCTTCGGGT
65 AAGCCTTCGGGT
* *
4497292 CATCTATAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
4497357 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
4497368 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCAGGAGCTTTTTGATATTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
4497433 AAGCCTTCGGGT
65 AAGCCTTCGGGT
*
4497445 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTACAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
*
4497510 AAGCCTTAGGGT
65 AAGCCTTCGGGT
4497522 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
4497587 AGCCTTCGGGT
66 AGCCTTCGGGT
4497598 CATCTGTAAGTCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTT
4497628 TCAACATTTC
Statistics
Matches: 696, Mismatches: 16, Indels: 12
0.96 0.02 0.02
Matches are distributed among these distances:
75 26 0.04
76 347 0.50
77 323 0.46
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:4497220 original size:153 final size:153
Alignment explanation
Indices: 4496834--4497627 Score: 1484
Period size: 153 Copynumber: 5.2 Consensus size: 153
4496824 CTATTTCTCA
*
4496834 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
4496899 AGCCTTCGGGTCATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTT
4496964 TGATG-TTTCAAAGCCTTCGGGT
131 TGATGTTTTCAAAGCCTTCGGGT
4496986 CATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
4497051 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTT
4497116 TGATGTTTTCAAAGCCTTCGGGT
131 TGATGTTTTCAAAGCCTTCGGGT
4497139 CATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
4497204 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTT
4497269 TGATGTTTTCAAAGCCTTCGGGT
131 TGATGTTTTCAAAGCCTTCGGGT
*
4497292 CATCTATAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
4497357 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCAGGAGCTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTT
*
4497422 TGATATTTTCAAAGCCTTCGGGT
131 TGATGTTTTCAAAGCCTTCGGGT
* *
4497445 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTACAA
1 CATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
*
4497510 AAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTT
65 AAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTT
4497574 TTGATGTTTTCAAAGCCTTCGGGT
130 TTGATGTTTTCAAAGCCTTCGGGT
*
4497598 CATCTGTAAGTCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTCCAGTGCATGATGTTT
4497628 TCAACATTTC
Statistics
Matches: 629, Mismatches: 11, Indels: 3
0.98 0.02 0.00
Matches are distributed among these distances:
152 133 0.21
153 452 0.72
154 44 0.07
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (153 bp):
CATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTT
TGATGTTTTCAAAGCCTTCGGGT
Found at i:4497766 original size:3 final size:3
Alignment explanation
Indices: 4497758--4497827 Score: 95
Period size: 3 Copynumber: 23.0 Consensus size: 3
4497748 TTCATTTTAA
**
4497758 ATT ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
4497806 ATT AGT AAT ATT ATTT ATT ATT
1 ATT ATT ATT ATT A-TT ATT ATT
4497828 TAAATATTAC
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
3 56 0.95
4 3 0.05
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:4497774 original size:15 final size:15
Alignment explanation
Indices: 4497756--4497836 Score: 80
Period size: 15 Copynumber: 5.6 Consensus size: 15
4497746 TTTTCATTTT
4497756 AAATTATTATTATTA
1 AAATTATTATTATTA
4497771 AAATTATTATTATT-
1 AAATTATTATTATTA
4497785 --ATTATTATTATTA
1 AAATTATTATTATTA
** *
4497798 TTATTATTATTAGTA
1 AAATTATTATTATTA
* *
4497813 ATATTATTTATTATTT
1 AAATTA-TTATTATTA
4497829 AAA-TATTA
1 AAATTATTA
4497837 CAAAGCCCAA
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
12 12 0.21
14 3 0.05
15 33 0.58
16 9 0.16
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (15 bp):
AAATTATTATTATTA
Found at i:4497833 original size:18 final size:17
Alignment explanation
Indices: 4497758--4497836 Score: 68
Period size: 18 Copynumber: 4.2 Consensus size: 17
4497748 TTCATTTTAA
*
4497758 ATTATTATTATTAAAATT
1 ATTATTATTATTTAAA-T
* *
4497776 ATTATTATTATTATTATT
1 ATTATTATTATT-TAAAT
4497794 ATTATTATTATTATTAGTAAT
1 ATTATTATTA-T-TTA--AAT
4497815 ATTATTTATTATTTAAAT
1 ATTA-TTATTATTTAAAT
4497833 ATTA
1 ATTA
4497837 CAAAGCCCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
18 30 0.60
19 3 0.06
20 4 0.08
21 7 0.14
22 6 0.12
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (17 bp):
ATTATTATTATTTAAAT
Found at i:4499373 original size:35 final size:35
Alignment explanation
Indices: 4499298--4499373 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 35
4499288 TTACTTAATT
*
4499298 TTTATTATTTTAATATATTTTAAATCATTACTTTA
1 TTTATTATTTTAATATATTATAAATCATTACTTTA
* * *
4499333 ATTATTGTTTTACTATATTATAAAT-ATATA-TATTA
1 TTTATTATTTTAATATATTATAAATCAT-TACT-TTA
4499368 TTTATT
1 TTTATT
4499374 TAATAATGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
34 3 0.09
35 31 0.91
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (35 bp):
TTTATTATTTTAATATATTATAAATCATTACTTTA
Found at i:4507172 original size:45 final size:46
Alignment explanation
Indices: 4507085--4507176 Score: 150
Period size: 45 Copynumber: 2.0 Consensus size: 46
4507075 TGAAAAAGCC
* *
4507085 TGAGTGCATCGACGCATGGTCTTGTGCATCGATGCATCAAATGCAT
1 TGAGTGCATCGACGCATGGTCGTGTGCATCGATGCATAAAATGCAT
*
4507131 TGAGTGCATCGATGCATGGT-GTGTGCATCGATGCATAAAATGCAT
1 TGAGTGCATCGACGCATGGTCGTGTGCATCGATGCATAAAATGCAT
4507176 T
1 T
4507177 CGATGTTTGG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
45 24 0.56
46 19 0.44
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.29
Consensus pattern (46 bp):
TGAGTGCATCGACGCATGGTCGTGTGCATCGATGCATAAAATGCAT
Found at i:4507219 original size:20 final size:20
Alignment explanation
Indices: 4507194--4507231 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4507184 TGGAAAATTA
4507194 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
4507214 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
4507232 CACTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:4510400 original size:24 final size:24
Alignment explanation
Indices: 4510335--4510401 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
4510325 ATTTGAATTA
*
4510335 TGTTATGATACCTGACATGGATTC
1 TGTTATGATACCTGACCTGGATTC
* * *
4510359 TGTTCTAATACCTTACCTGGATTC
1 TGTTATGATACCTGACCTGGATTC
*
4510383 TGTTATGATATCTGACCTG
1 TGTTATGATACCTGACCTG
4510402 AATTGTAACA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.40
Consensus pattern (24 bp):
TGTTATGATACCTGACCTGGATTC
Found at i:4515348 original size:18 final size:18
Alignment explanation
Indices: 4515308--4515353 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
4515298 AAAGAAGTGG
4515308 ATTAATATTTAAAAAATA
1 ATTAATATTTAAAAAATA
* * * *
4515326 TTTAAAATTTAAATATTA
1 ATTAATATTTAAAAAATA
4515344 ATTAATATTT
1 ATTAATATTT
4515354 TTTTTATTTT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
ATTAATATTTAAAAAATA
Found at i:4519505 original size:24 final size:26
Alignment explanation
Indices: 4519461--4519518 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
4519451 AGTTTGAACA
4519461 GTTTAA-TTTTTTAAGGTGTGTTTAT
1 GTTTAATTTTTTTAAGGTGTGTTTAT
4519486 GTTTAATTTTTTTAAGGTGT-TTT-T
1 GTTTAATTTTTTTAAGGTGTGTTTAT
4519510 GTTTAATTT
1 GTTTAATTT
4519519 ATATTTGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 10 0.31
25 9 0.28
26 13 0.41
ACGTcount: A:0.19, C:0.00, G:0.17, T:0.64
Consensus pattern (26 bp):
GTTTAATTTTTTTAAGGTGTGTTTAT
Found at i:4521346 original size:5 final size:5
Alignment explanation
Indices: 4521338--4521365 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
4521328 TTTTATAAAG
4521338 TTTTC TTTTC TTTTC TTTTC TTTTC TTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTT
4521366 AAAATGCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:4525077 original size:99 final size:99
Alignment explanation
Indices: 4524939--4525137 Score: 335
Period size: 99 Copynumber: 2.0 Consensus size: 99
4524929 AAATTTATTC
* * *
4524939 AAATCTCATGCCCCAATATTAAGAAAGAAATTATTTGATCTTCACATATCACCCATATGTTCATT
1 AAATCCCATGCCCCAATATTAAGAAAGAAATTATATGATCTTCACATAACACCCATATGTTCATT
4525004 TGAATGATCTAAATTTAAAAACTGATACGAGTAG
66 TGAATGATCTAAATTTAAAAACTGATACGAGTAG
* *
4525038 AAATCCCATTCCCCAATATTAAGAAAGAAATTATATGATCTTCACATAACACCTATATGTTCATT
1 AAATCCCATGCCCCAATATTAAGAAAGAAATTATATGATCTTCACATAACACCCATATGTTCATT
* *
4525103 TGAATTATCTAAATTTGAAAACTGATACGAGTAG
66 TGAATGATCTAAATTTAAAAACTGATACGAGTAG
4525137 A
1 A
4525138 TGGAGCAAAC
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
99 93 1.00
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (99 bp):
AAATCCCATGCCCCAATATTAAGAAAGAAATTATATGATCTTCACATAACACCCATATGTTCATT
TGAATGATCTAAATTTAAAAACTGATACGAGTAG
Found at i:4527422 original size:17 final size:18
Alignment explanation
Indices: 4527383--4527429 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
4527373 TGTTTCTGAG
*
4527383 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTATGAA
*
4527401 GGAATTGGAATCTAT-CA
1 GGAATTGGAATCTATGAA
4527418 GGAATTGGAATC
1 GGAATTGGAATC
4527430 CAATTCCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.34, C:0.09, G:0.30, T:0.28
Consensus pattern (18 bp):
GGAATTGGAATCTATGAA
Found at i:4527803 original size:20 final size:19
Alignment explanation
Indices: 4527757--4527805 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
4527747 ATGACTGACA
* *
4527757 AATTCGCAACGCGATCTCG
1 AATTCGCAACGCGAACTCC
4527776 AATTCGCAACGCGAACTCC
1 AATTCGCAACGCGAACTCC
4527795 AATTTCGCAAC
1 AA-TTCGCAAC
4527806 TCATTTTCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.31, C:0.33, G:0.16, T:0.20
Consensus pattern (19 bp):
AATTCGCAACGCGAACTCC
Found at i:4527881 original size:21 final size:21
Alignment explanation
Indices: 4527839--4527885 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
4527829 AATATGTAAA
**
4527839 TCGCATTGCGATTTTATGAAT
1 TCGCATTGCGATTTTACAAAT
* *
4527860 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
4527881 TCGCA
1 TCGCA
4527886 ACGCGAATAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:4527946 original size:20 final size:20
Alignment explanation
Indices: 4527921--4528049 Score: 100
Period size: 20 Copynumber: 6.4 Consensus size: 20
4527911 AATCTGTAAA
* *
4527921 TCGCAACGCGATTTCCAAAT
1 TCGCAACACGATTTACAAAT
*
4527941 TCGCAACATGATTTACAAAT
1 TCGCAACACGATTTACAAAT
****
4527961 TCGCGTTGCGATTTACAAAT
1 TCGCAACACGATTTACAAAT
*
4527981 TCGAAACACTGAATTT-CAAAT
1 TCGCAACAC-G-ATTTACAAAT
*
4528002 TCGCAACTCGATTT-CTAAAT
1 TCGCAACACGATTTAC-AAAT
* ***
4528022 TCGCAACTCGATTTTTGAAT
1 TCGCAACACGATTTACAAAT
4528042 TCGCAACA
1 TCGCAACA
4528050 GGTTTTATTT
Statistics
Matches: 87, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
19 5 0.06
20 65 0.75
21 13 0.15
22 4 0.05
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (20 bp):
TCGCAACACGATTTACAAAT
Found at i:4527983 original size:40 final size:41
Alignment explanation
Indices: 4527928--4528005 Score: 115
Period size: 40 Copynumber: 1.9 Consensus size: 41
4527918 AAATCGCAAC
* *
4527928 GCGATTTCCAAATTCGCAACA-TG-ATTTACAAATTCGCGTT
1 GCGATTTACAAATTCGAAACACTGAATTT-CAAATTCGCGTT
4527968 GCGATTTACAAATTCGAAACACTGAATTTCAAATTCGC
1 GCGATTTACAAATTCGAAACACTGAATTTCAAATTCGC
4528006 AACTCGATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
40 19 0.56
41 11 0.32
42 4 0.12
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (41 bp):
GCGATTTACAAATTCGAAACACTGAATTTCAAATTCGCGTT
Found at i:4528011 original size:101 final size:101
Alignment explanation
Indices: 4527857--4528049 Score: 223
Period size: 101 Copynumber: 1.9 Consensus size: 101
4527847 CGATTTTATG
* * * * *
4527857 AATTCGCGTTGCGATTTTCCAAATTCGCAACGCGAATATGTAAATCATAACTCGAATCTGTAAA-
1 AATTCGCGTTGCGATTTTACAAATTCGAAACACGAATATGTAAATCACAACTCG-ATCTCTAAAT
4527921 TCGCAACGCGATTTCCAAATTCGCAACATGATTTACA
65 TCGCAACGCGATTTCCAAATTCGCAACATGATTTACA
* *
4527958 AATTCGCGTTGCGA-TTTACAAATTCGAAACACTGAAT-T-TCAAATTCGCAACTCGATTTCTAA
1 AATTCGCGTTGCGATTTTACAAATTCGAAACAC-GAATATGT-AAA-TCACAACTCGATCTCTAA
* ***
4528020 ATTCGCAACTCGATTTTTGAATTCGCAACA
63 ATTCGCAACGCGATTTCCAAATTCGCAACA
4528050 GGTTTTATTT
Statistics
Matches: 77, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
99 1 0.01
100 26 0.34
101 50 0.65
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (101 bp):
AATTCGCGTTGCGATTTTACAAATTCGAAACACGAATATGTAAATCACAACTCGATCTCTAAATT
CGCAACGCGATTTCCAAATTCGCAACATGATTTACA
Found at i:4528014 original size:41 final size:39
Alignment explanation
Indices: 4527921--4528024 Score: 104
Period size: 41 Copynumber: 2.6 Consensus size: 39
4527911 AATCTGTAAA
* *
4527921 TCGCAACGCGATTTCCAAATTCGCAACATGATTTACAAAT
1 TCGCAACTCGATTT-CAAATTCGAAACATGATTTACAAAT
**
4527961 TCGC-GTTGCGATTTACAAATTCGAAACACTGAATTT-CAAAT
1 TCGCAACT-CGATTT-CAAATTCGAAACA-TG-ATTTACAAAT
4528002 TCGCAACTCGATTTCTAAATTCG
1 TCGCAACTCGATTTC-AAATTCG
4528025 CAACTCGATT
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
40 23 0.44
41 24 0.46
42 5 0.10
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (39 bp):
TCGCAACTCGATTTCAAATTCGAAACATGATTTACAAAT
Found at i:4528859 original size:12 final size:12
Alignment explanation
Indices: 4528838--4528871 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
4528828 ACCACATTTT
*
4528838 CAATACCAAACA
1 CAATATCAAACA
4528850 CAATATCAAACA
1 CAATATCAAACA
*
4528862 CAATCTCAAA
1 CAATATCAAA
4528872 ACCCACAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:4529719 original size:24 final size:24
Alignment explanation
Indices: 4529685--4529738 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
4529675 CTGAAACATC
4529685 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
4529709 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
4529733 ATCAAA
1 ATCAAA
4529739 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:4529752 original size:24 final size:24
Alignment explanation
Indices: 4529685--4529752 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
4529675 CTGAAACATC
* * *
4529685 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
4529709 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
4529733 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
4529753 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:4529885 original size:12 final size:12
Alignment explanation
Indices: 4529864--4529897 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
4529854 GGTTGTGGGT
*
4529864 TTTGAGATTGTG
1 TTTGATATTGTG
4529876 TTTGATATTGTG
1 TTTGATATTGTG
*
4529888 TTTGGTATTG
1 TTTGATATTG
4529898 AAAATGTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:4540321 original size:18 final size:18
Alignment explanation
Indices: 4540298--4540347 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
4540288 AACATTTGTG
4540298 TTGCGAAAATAAAACATA
1 TTGCGAAAATAAAACATA
* *
4540316 TTGCGAACATAAAACATG
1 TTGCGAAAATAAAACATA
4540334 TTGC-AAAATTAAAA
1 TTGCGAAAA-TAAAA
4540348 TTCGTGTTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 3 0.11
18 25 0.89
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (18 bp):
TTGCGAAAATAAAACATA
Found at i:4540470 original size:81 final size:80
Alignment explanation
Indices: 4540356--4540505 Score: 201
Period size: 81 Copynumber: 1.9 Consensus size: 80
4540346 AATTCGTGTT
4540356 GCGAATTCGAAAATCGAGTTACGAATTCAGAAATCGAGTTGCAAATTTGAAATTCAGTGTTGCGA
1 GCGAATTCGAAAATCGAGTTACGAATTCAGAAATCGAGTTGCAAATTTG-AATTCAGTGTTGCGA
4540421 ATTTGTAAATCGCAAC
65 ATTTGTAAATCGCAAC
* * * * ** * * * *
4540437 GCGAATTTGGAAATCGCGTTGCGAATTTGGAAATCGCGTTGCGAATTTGACTTCTGTGTTGCGAA
1 GCGAATTCGAAAATCGAGTTACGAATTCAGAAATCGAGTTGCAAATTTGAATTCAGTGTTGCGAA
4540502 TTTG
66 TTTG
4540506 ACTTCTGTGT
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
80 18 0.31
81 41 0.69
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (80 bp):
GCGAATTCGAAAATCGAGTTACGAATTCAGAAATCGAGTTGCAAATTTGAATTCAGTGTTGCGAA
TTTGTAAATCGCAAC
Found at i:4540484 original size:20 final size:20
Alignment explanation
Indices: 4540353--4540485 Score: 124
Period size: 20 Copynumber: 6.6 Consensus size: 20
4540343 TAAAATTCGT
* * *
4540353 GTTGCGAATTCGAAAATCGA
1 GTTGCGAATTTGGAAATCGC
* ** *
4540373 GTTACGAATTCAGAAATCGA
1 GTTGCGAATTTGGAAATCGC
* *
4540393 GTTGCAAATTT-GAAATTCAGT
1 GTTGCGAATTTGGAAA-TC-GC
*
4540414 GTTGCGAATTTGTAAATCGC
1 GTTGCGAATTTGGAAATCGC
***
4540434 AACGCGAATTTGGAAATCGC
1 GTTGCGAATTTGGAAATCGC
4540454 GTTGCGAATTTGGAAATCGC
1 GTTGCGAATTTGGAAATCGC
4540474 GTTGCGAATTTG
1 GTTGCGAATTTG
4540486 ACTTCTGTGT
Statistics
Matches: 93, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
19 4 0.04
20 73 0.78
21 13 0.14
22 3 0.03
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (20 bp):
GTTGCGAATTTGGAAATCGC
Found at i:4540497 original size:20 final size:20
Alignment explanation
Indices: 4540474--4540517 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
4540464 TGGAAATCGC
4540474 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTCTGT
4540494 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTCTGT
4540514 GTTG
1 GTTG
4540518 TAATTTACGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.14, C:0.14, G:0.27, T:0.45
Consensus pattern (20 bp):
GTTGCGAATTTGACTTCTGT
Found at i:4540498 original size:40 final size:39
Alignment explanation
Indices: 4540353--4540505 Score: 126
Period size: 40 Copynumber: 3.8 Consensus size: 39
4540343 TAAAATTCGT
* * * * ** *
4540353 GTTGCGAATTCGAAAATCGAGTTACGAATTCAGAAATCGA
1 GTTGCGAATTTG-AATTCGTGTTGCGAATTTGGAAATCGC
* *
4540393 GTTGCAAATTTGAAATTCAGTGTTGCGAATTTGTAAATCGC
1 GTTGCGAATTTG-AATTC-GTGTTGCGAATTTGGAAATCGC
*** * *
4540434 AACGCGAATTTGGAAATCGCGTTGCGAATTTGGAAATCGC
1 GTTGCGAATTT-GAATTCGTGTTGCGAATTTGGAAATCGC
*
4540474 GTTGCGAATTTGACTTCTGTGTTGCGAATTTG
1 GTTGCGAATTTGAATTC-GTGTTGCGAATTTG
4540506 ACTTCTGTGT
Statistics
Matches: 88, Mismatches: 22, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
39 4 0.05
40 56 0.64
41 27 0.31
42 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (39 bp):
GTTGCGAATTTGAATTCGTGTTGCGAATTTGGAAATCGC
Found at i:4541060 original size:11 final size:11
Alignment explanation
Indices: 4541044--4541069 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4541034 ATCTGACCTG
4541044 AAATAATAAAA
1 AAATAATAAAA
4541055 AAATAATAAAA
1 AAATAATAAAA
4541066 AAAT
1 AAAT
4541070 TGACCCAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
AAATAATAAAA
Found at i:4546942 original size:45 final size:46
Alignment explanation
Indices: 4546850--4546957 Score: 157
Period size: 45 Copynumber: 2.4 Consensus size: 46
4546840 TGCACATACC
** *
4546850 ATGCATCGATGCACTGAGGATTTTATGAAAACATCGAATGCATTTG
1 ATGCATCGATGCACTCTGGATTTTATGAAAACATCGAATGCACTTG
*
4546896 ATGCATCGATGCACTCTGGCTATTT-TG-AAACATCGAATGCACTTG
1 ATGCATCGATGCACTCTGGAT-TTTATGAAAACATCGAATGCACTTG
4546941 ATGCATCGATGCACTCT
1 ATGCATCGATGCACTCT
4546958 TAGTGCACCG
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
45 34 0.60
46 20 0.35
47 3 0.05
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (46 bp):
ATGCATCGATGCACTCTGGATTTTATGAAAACATCGAATGCACTTG
Found at i:4546954 original size:17 final size:19
Alignment explanation
Indices: 4546926--4546974 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
4546916 TATTTTGAAA
4546926 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
4546944 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
4546963 CACCGATGCACT
1 CATCGATGCACT
4546975 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:4548742 original size:15 final size:15
Alignment explanation
Indices: 4548705--4548745 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
4548695 CTACATGGAG
*
4548705 CGATGAAAAGGGTTC
1 CGATGAAGAGGGTTC
4548720 CGATGAAGAGGGTTC
1 CGATGAAGAGGGTTC
*
4548735 TGATGAAGAGG
1 CGATGAAGAGG
4548746 AACAAGAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.32, C:0.10, G:0.39, T:0.20
Consensus pattern (15 bp):
CGATGAAGAGGGTTC
Found at i:4552788 original size:42 final size:43
Alignment explanation
Indices: 4552740--4552832 Score: 120
Period size: 43 Copynumber: 2.2 Consensus size: 43
4552730 TTTGTGCTTC
*
4552740 ATGCATCGATACACCTA-ACA-GTGCATCGATGCA-TCCTTGAAT
1 ATGCATCGATACA-CTAGA-AGGTGCATCGATGCACGCCTTGAAT
*
4552782 GTGCATCGATACACTATGAAGGTGCATCGATGCACGCCTTGAAT
1 ATGCATCGATACACTA-GAAGGTGCATCGATGCACGCCTTGAAT
4552826 ATGCATC
1 ATGCATC
4552833 AATGCACAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
41 3 0.07
42 13 0.30
43 14 0.32
44 14 0.32
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (43 bp):
ATGCATCGATACACTAGAAGGTGCATCGATGCACGCCTTGAAT
Found at i:4552806 original size:21 final size:21
Alignment explanation
Indices: 4552741--4552812 Score: 69
Period size: 21 Copynumber: 3.4 Consensus size: 21
4552731 TTGTGCTTCA
*
4552741 TGCATCGATACACC-T-AACAG
1 TGCATCGATACACCTTGAA-GG
* *
4552761 TGCATCGATGCATCCTTGAATG
1 TGCATCGATACA-CCTTGAAGG
4552783 TGCATCGATACA-CTATGAAGG
1 TGCATCGATACACCT-TGAAGG
4552804 TGCATCGAT
1 TGCATCGAT
4552813 GCACGCCTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
20 13 0.30
21 16 0.36
22 13 0.30
23 2 0.05
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (21 bp):
TGCATCGATACACCTTGAAGG
Found at i:4552830 original size:23 final size:22
Alignment explanation
Indices: 4552760--4552839 Score: 83
Period size: 23 Copynumber: 3.6 Consensus size: 22
4552750 ACACCTAACA
*
4552760 GTGCATCGATGCATCCTTGAAT
1 GTGCATCGATGCACCCTTGAAT
* *
4552782 GTGCATCGAT--ACACTATGAAG
1 GTGCATCGATGCACCCT-TGAAT
4552803 GTGCATCGATGCACGCCTTGAAT
1 GTGCATCGATGCAC-CCTTGAAT
* *
4552826 ATGCATCAATGCAC
1 GTGCATCGATGCAC
4552840 AAGACCATGC
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
20 3 0.06
21 14 0.30
22 10 0.21
23 18 0.38
24 2 0.04
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACCCTTGAAT
Found at i:4554549 original size:65 final size:64
Alignment explanation
Indices: 4554437--4554595 Score: 178
Period size: 65 Copynumber: 2.5 Consensus size: 64
4554427 AAATAAATTG
* * * *
4554437 AACATCGAATGTATTTCATGCATCGATGTACATACCATACATCGATGCACTGAGGATT-TTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACATACCATACATCGATGCACTCAGG-TTATTATG-
4554501 A
64 A
* * * * * * *
4554502 AACATCGAATGCATTTGATGCATCGATGCACCTGCTATGCATTGATGCACTCTGGTTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCACATACCATACATCGATGCACTCAGGTTATTATGA
*
4554566 AACATCGAATGCACTTGATGCATC-ATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
4554596 TCTTAGTACA
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
63 6 0.07
64 26 0.32
65 49 0.60
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGCACATACCATACATCGATGCACTCAGGTTATTATGA
Found at i:4560441 original size:21 final size:21
Alignment explanation
Indices: 4560399--4560442 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
4560389 ACTCCGGGAG
* *
4560399 CTAGTTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
4560420 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
4560441 CT
1 CT
4560443 CCTCCGGCAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.39, G:0.16, T:0.36
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:4560796 original size:14 final size:16
Alignment explanation
Indices: 4560765--4560796 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
4560755 TTGGATTGTT
4560765 TTTTTATGTTTCTGGA
1 TTTTTATGTTTCTGGA
4560781 TTTTT-TGTTT-TGGA
1 TTTTTATGTTTCTGGA
4560795 TT
1 TT
4560797 GTTAAATACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 5 0.31
16 5 0.31
ACGTcount: A:0.09, C:0.03, G:0.19, T:0.69
Consensus pattern (16 bp):
TTTTTATGTTTCTGGA
Found at i:4560852 original size:2 final size:2
Alignment explanation
Indices: 4560845--4560909 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
4560835 TTTTAAACTT
4560845 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
4560887 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
4560910 TGTTTGGTTG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4561129 original size:15 final size:15
Alignment explanation
Indices: 4561109--4561138 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4561099 TTTTAATGTC
4561109 TTTTTGATTTAACAA
1 TTTTTGATTTAACAA
4561124 TTTTTGATTTAACAA
1 TTTTTGATTTAACAA
4561139 AAAGGGGGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (15 bp):
TTTTTGATTTAACAA
Found at i:4561559 original size:29 final size:29
Alignment explanation
Indices: 4561517--4561581 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
4561507 ATGCACTAAG
*
4561517 GCACTAATGCACCATGGGTTTGAATCGAT
1 GCACTGATGCACCATGGGTTTGAATCGAT
4561546 GCACTGATGCACCATGGGTTTGAATCGAT
1 GCACTGATGCACCATGGGTTTGAATCGAT
4561575 GCACTGA
1 GCACTGA
4561582 CGCTCCCAGC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (29 bp):
GCACTGATGCACCATGGGTTTGAATCGAT
Found at i:4562799 original size:4 final size:4
Alignment explanation
Indices: 4562792--4562855 Score: 51
Period size: 4 Copynumber: 16.0 Consensus size: 4
4562782 AAGATAAAAC
* * *
4562792 AAAT AAAT AAAT AAAT AAGAT -AAT AAAC AAAT AAAAT AAAC AAAG AAA-
1 AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT
* *
4562840 CAAG AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT
4562856 TATAAAAAAC
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
3 4 0.08
4 39 0.80
5 6 0.12
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.17
Consensus pattern (4 bp):
AAAT
Found at i:4562818 original size:16 final size:16
Alignment explanation
Indices: 4562797--4562855 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 16
4562787 AAAACAAATA
4562797 AATAAATAAATAAGAT
1 AATAAATAAATAAGAT
* *
4562813 AATAAACAAATAAAAT
1 AATAAATAAATAAGAT
* * *
4562829 AAACAAAGAAACAAGA-
1 -AATAAATAAATAAGAT
4562845 AATAAATAAAT
1 AATAAATAAAT
4562856 TATAAAAAAC
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
15 8 0.24
16 14 0.42
17 11 0.33
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.17
Consensus pattern (16 bp):
AATAAATAAATAAGAT
Found at i:4565011 original size:117 final size:116
Alignment explanation
Indices: 4564759--4565161 Score: 472
Period size: 117 Copynumber: 3.5 Consensus size: 116
4564749 TCATTCGCTG
* * * * *
4564759 TGAAGTTGAGCTTTGAATTGGATATCCTTCATCGTGAAGTTAAAATCCAATCTTGTGTAG--GT-
1 TGAAGTTGAGCCTCGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAATCTTGAGTTGTTGTG
* * * * * * * *
4564821 AAGCACAATATCCTTCTTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTG
66 GA-CACGATATCCTTCATCGTGAAGTTAAAATCGTGGGTGGCCCCTTCGTTA
*
4564873 TGAAGTTGAGCCTCAAATTGGATATCCTTCATCGTGAAGTTGAAATCCAATCTTGAGTTGCTTGT
1 TGAAGTTGAGCCTCGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAATCTTGAGTTG-TTGT
* * *
4564938 GGACACGATATCCTTCATCGTGAAGTTTAAATTGTGGGTGGCCCCTTCATTA
65 GGACACGATATCCTTCATCGTGAAGTTAAAATCGTGGGTGGCCCCTTCGTTA
* * *
4564990 TGAAGTTGAGCCTTGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAATCATGAGTTTTTTGT
1 TGAAGTTGAGCCTCGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAATCTTGAG-TTGTTGT
* ** * * * *
4565055 GGACACGTTATCCTTTGTTGTGAAGTTAAAATCATAGGTGTCCCCTTCGTTA
65 GGACACGATATCCTTCATCGTGAAGTTAAAATCGTGGGTGGCCCCTTCGTTA
* * *
4565107 TGAAGTTGAACATCGAATTGGATATCTTTCATCGTGAAGTAT-AAATCCAATCTTG
1 TGAAGTTGAGCCTCGAATTGGATATCCTTCATCGTGAAGT-TGAAATCCAATCTTG
4565162 TTTGATTTTG
Statistics
Matches: 248, Mismatches: 35, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
114 54 0.22
117 190 0.77
118 4 0.02
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (116 bp):
TGAAGTTGAGCCTCGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAATCTTGAGTTGTTGTG
GACACGATATCCTTCATCGTGAAGTTAAAATCGTGGGTGGCCCCTTCGTTA
Found at i:4566154 original size:13 final size:13
Alignment explanation
Indices: 4566138--4566163 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4566128 TTTTTTGTTC
4566138 TTTTCTTTTTCTT
1 TTTTCTTTTTCTT
4566151 TTTTCTTTTTCTT
1 TTTTCTTTTTCTT
4566164 CTTCAACTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTCTTTTTCTT
Found at i:4574851 original size:65 final size:66
Alignment explanation
Indices: 4574684--4574843 Score: 286
Period size: 66 Copynumber: 2.4 Consensus size: 66
4574674 AAATTGAATT
*
4574684 TTGAATGCATTTAGTGCACCGATGCACAAGCCATGCATCGATACACCCATAAATATTTTTGAAAC
1 TTGAATGCATTCAGTGCACCGATGCACAAGCCATGCATCGATACACCCATAAATATTTTTGAAAC
4574749 A
66 A
*
4574750 TCGAATGCATTCAGTGCACCGATGCACAAGCCATGCATCGATACACCCATAAATA-TTTTGAAAC
1 TTGAATGCATTCAGTGCACCGATGCACAAGCCATGCATCGATACACCCATAAATATTTTTGAAAC
4574814 A
66 A
*
4574815 TTGAATGCATTCAGTGCGCCGATGCACAA
1 TTGAATGCATTCAGTGCACCGATGCACAA
4574844 TACATGCACC
Statistics
Matches: 90, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
65 37 0.41
66 53 0.59
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (66 bp):
TTGAATGCATTCAGTGCACCGATGCACAAGCCATGCATCGATACACCCATAAATATTTTTGAAAC
A
Found at i:4574857 original size:19 final size:19
Alignment explanation
Indices: 4574833--4574898 Score: 114
Period size: 19 Copynumber: 3.5 Consensus size: 19
4574823 ATTCAGTGCG
4574833 CCGATGCACAATACATGCA
1 CCGATGCACAATACATGCA
4574852 CCGATGCACAATACATGCA
1 CCGATGCACAATACATGCA
*
4574871 TCGATGCACAATACATGCA
1 CCGATGCACAATACATGCA
*
4574890 TCGATGCAC
1 CCGATGCAC
4574899 CCTGGTTATT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 46 1.00
ACGTcount: A:0.35, C:0.30, G:0.17, T:0.18
Consensus pattern (19 bp):
CCGATGCACAATACATGCA
Found at i:4580082 original size:23 final size:22
Alignment explanation
Indices: 4580049--4580150 Score: 116
Period size: 23 Copynumber: 4.5 Consensus size: 22
4580039 CACTATCTAG
4580049 TGCATCGATGCATCCTTTGAATA
1 TGCATCGATGCATCC-TTGAATA
*
4580072 TGTATCGATGCATCCTTTGAATA
1 TGCATCGATGCATCC-TTGAATA
* * *
4580095 TGCATCGATACAT-CATGAAGA
1 TGCATCGATGCATCCTTGAATA
* *
4580116 TGCACCGATGCAATCCTTGAATG
1 TGCATCGATGC-ATCCTTGAATA
4580139 TGCATCGATGCA
1 TGCATCGATGCA
4580151 CTATCCTGTG
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
21 14 0.21
22 4 0.06
23 48 0.73
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (22 bp):
TGCATCGATGCATCCTTGAATA
Found at i:4582866 original size:65 final size:65
Alignment explanation
Indices: 4582740--4582947 Score: 212
Period size: 64 Copynumber: 3.2 Consensus size: 65
4582730 TTCAAAGGGA
* * ** ** *
4582740 TGCACCGATGCAC-TACTTCATGCATCGATGCACTCCTAATTAAATTG-AATTTTGAATGCATTT
1 TGCACCGATGCACAAAC--CATGCATCGATGCACCCCTAATTATTTTGAAACATCGAATGCATTT
4582803 AG
64 AG
* *
4582805 TGCACCGATGCACAAACCATGCATCGATGCACCCCTAAATATTTTGAAACATCGAATGCATTCAG
1 TGCACCGATGCACAAACCATGCATCGATGCACCCCTAATTATTTTGAAACATCGAATGCATTTAG
* * **
4582870 TGCACCTATCCACAAGA-CATGCATCGATGCA-CCCTGGTTATTTTGAAACATCGAA-GCTGATT
1 TGCACCGATGCACAA-ACCATGCATCGATGCACCCCTAATTATTTTGAAACATCGAATGC--ATT
4582932 T-G
63 TAG
4582934 TGCACCGATGCACA
1 TGCACCGATGCACA
4582948 CCCTAGTGCA
Statistics
Matches: 121, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
63 2 0.02
64 59 0.49
65 57 0.47
66 3 0.02
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.27
Consensus pattern (65 bp):
TGCACCGATGCACAAACCATGCATCGATGCACCCCTAATTATTTTGAAACATCGAATGCATTTAG
Found at i:4585380 original size:18 final size:17
Alignment explanation
Indices: 4585357--4585395 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
4585347 TATTGTAATT
4585357 ATAATTGCAGACTATTTA
1 ATAATTG-AGACTATTTA
**
4585375 ATAATTGAGTTTATTTA
1 ATAATTGAGACTATTTA
4585392 ATAA
1 ATAA
4585396 GTAAACATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (17 bp):
ATAATTGAGACTATTTA
Found at i:4590767 original size:23 final size:23
Alignment explanation
Indices: 4590741--4590813 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
4590731 ATATTTTACA
*
4590741 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* *
4590764 ATATAAACGCTCCCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
4590787 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
4590810 ATAT
1 ATAT
4590814 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:4591257 original size:489 final size:490
Alignment explanation
Indices: 4590339--4592130 Score: 3361
Period size: 489 Copynumber: 3.7 Consensus size: 490
4590329 TTATAATATG
* *
4590339 TTGAAAGTGTCTATATATTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCTATA-CTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
4590404 TTCAA--TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
65 TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
* *
4590467 ACAAAAAACTATTTGATCGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
130 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
4590532 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
195 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
4590597 TATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
260 TATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
* * *
4590662 TCAAAATATAACCTTAAATTAATATTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAAAGA
325 TCAAAATATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
* *
4590727 ATAGATATTTTACAATATAAGCACTACCTATTACATTATATAAACGCTCCCTATTACATTATATA
390 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
4590792 AGCGCTACCTATTACATCATATTTTTACCTATTATA
455 AGCGCTACCTATTACATCATATTTTTACCTATTATA
*
4590828 TTGAAAGTGTCTATACTTTTTATAAAAATGATCGATAC-TTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
*
4590892 TTAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
4590957 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
4591022 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
196 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
4591087 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
261 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
4591152 CAAAATATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
326 CAAAATATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
4591217 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
391 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
4591282 GCGCTACCTATTACATCATATTTTTACCTATTATA
456 GCGCTACCTATTACATCATATTTTTACCTATTATA
4591317 TTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
*
4591382 TCAATTTTTTTTAATAGTTTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
*
4591447 CAAAAAATTATTTGATTATTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
4591512 TAACCAAAGATAATAATAAATATGT-A-ATATATGTTTATTGTTTTTAATTTAATAAT-A-ATAT
196 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
4591573 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
261 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
*
4591638 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
326 CAAAATATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
*
4591703 TAGATACTTTACAATATAAGCACTACCTATTATA-T-TATAAACGCTACCTATTACATTATATAA
391 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
4591766 GCGCTACCTATTACATCATATTTTTACCTA-TATA
456 GCGCTACCTATTACATCATATTTTTACCTATTATA
4591800 TTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
4591865 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
4591930 CAAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
131 C-AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
4591995 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
195 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
4592060 TATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
260 TATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
4592125 TCAAAA
325 TCAAAA
4592131 GATGTACATA
Statistics
Matches: 1277, Mismatches: 18, Indels: 17
0.97 0.01 0.01
Matches are distributed among these distances:
483 134 0.10
484 146 0.11
485 2 0.00
486 196 0.15
487 31 0.02
488 125 0.10
489 465 0.36
490 178 0.14
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.41
Consensus pattern (490 bp):
TTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
CAAAATATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
GCGCTACCTATTACATCATATTTTTACCTATTATA
Done.