Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009585.1 Hibiscus syriacus cultivar Beakdansim tig00116962_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: 8285662
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 20 of 35
Found at i:4254684 original size:4 final size:4
Alignment explanation
Indices: 4254677--4254709 Score: 57
Period size: 4 Copynumber: 8.0 Consensus size: 4
4254667 ATATAATGGT
4254677 AATA AATAA AATA AATA AATA AATA AATA AATA
1 AATA AAT-A AATA AATA AATA AATA AATA AATA
4254710 GCTATAATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:4254687 original size:26 final size:27
Alignment explanation
Indices: 4254601--4254687 Score: 88
Period size: 27 Copynumber: 3.2 Consensus size: 27
4254591 AATATAGAAT
* *
4254601 ATAAAAATAATATATATGATGGTAAT-A
1 ATAAAAA-GATATATATAATGGTAATAA
* * * *
4254628 ATAATAAAGATATAAACATTGGGAA-AA
1 ATAA-AAAGATATATATAATGGTAATAA
4254655 ATAAAAAGATATATATAATGGTAATAA
1 ATAAAAAGATATATATAATGGTAATAA
4254682 ATAAAA
1 ATAAAA
4254688 TAAATAAATA
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
26 16 0.34
27 28 0.60
28 3 0.06
ACGTcount: A:0.60, C:0.01, G:0.11, T:0.28
Consensus pattern (27 bp):
ATAAAAAGATATATATAATGGTAATAA
Found at i:4254973 original size:14 final size:14
Alignment explanation
Indices: 4254954--4254981 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4254944 TAACGATGAT
4254954 TATGTATATATATA
1 TATGTATATATATA
4254968 TATGTATATATATA
1 TATGTATATATATA
4254982 ATAAATAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
TATGTATATATATA
Found at i:4256154 original size:19 final size:18
Alignment explanation
Indices: 4256126--4256162 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
4256116 AAAAGAAAAG
4256126 TATAAATATATATATTAT
1 TATAAATATATATATTAT
*
4256144 TATATAATATATTTATTAT
1 TATA-AATATATATATTAT
4256163 ATGATATGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TATAAATATATATATTAT
Found at i:4256161 original size:16 final size:17
Alignment explanation
Indices: 4256133--4256169 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
4256123 AAGTATAAAT
4256133 ATATATATTATTATATA
1 ATATATATTATTATATA
*
4256150 ATATAT-TTATTATATG
1 ATATATATTATTATATA
4256166 ATAT
1 ATAT
4256170 GGTCGAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
ATATATATTATTATATA
Found at i:4257590 original size:433 final size:434
Alignment explanation
Indices: 4256783--4257652 Score: 1580
Period size: 433 Copynumber: 2.0 Consensus size: 434
4256773 TCATCTTCAA
*
4256783 TCATTAGGGTGAGTTTACTCTTGTGATCCTACGTGTATGGTCTCATATAACGAGATCGTTGTGGT
1 TCATTAGGGTGAGTTTACTCTTGTGATCCTACGTGTATGGTCTCACATAACGAGATCGTTGTGGT
* *
4256848 ATCTGGTAATGATGCAATGATGATTATTTTTTAATAATGTTGTCTTTATGACATGTTTTCTTTTA
66 ATCTGGTAATGATGCAATGATAATTATTTTTTAATAATGTTGTCTTTATGACATGTTTTCTTATA
4256913 TTTTTTTTATATGTTTCATCTATCTTTTGGTAAGTTTTTTGTCAATTGATCGTTATTTTTGTTTA
131 TTTTTTTTATATGTTTCATCTATCTTTTGGTAAGTTTTTTGTCAATTGATCGTTATTTTTGTTTA
*
4256978 TCATTTTTATCATGGTTGGATTTGACATCGCAATCAAAATAGCGCTCGTTTGTTATAATGTTGAT
196 TAATTTTTATCATGGTTGGATTTGACATCGCAATCAAAATAGCGCTCGTTTGTTATAATGTTGAT
* *
4257043 ATTCTCTACTTTGGACCCTCGGATTAGATTTGGATACGTAATTTGCATTTGTGGATAGTTTTATC
261 ATTCTCTACTTTGGACCCTCGGATTAGATTTGGATACGCAATTTCCATTTGTGGATAGTTTTATC
4257108 ACGTCGCTTGATCTTGATTTACGTTTTGTCGGCGGTCTTTCAATAGCTTGATCCTCTTTTGTGGT
326 ACGTCGCTTGATCTTGATTTACGTTTTGTCGGCGGTCTTTCAATAGCTTGATCCTCTTTTGTGGT
*
4257173 TCGTTTTGTCGATACGGCCAGATATGTTCGTATCTACCTTTGAT
391 TCGTTTTGCCGATACGGCCAGATATGTTCGTATCTACCTTTGAT
*
4257217 TCATTAGGGTGAGTTTACTCTTGTGATCCTACGTGTATGGTCTCACATAACGAGGTCGTTGTGGT
1 TCATTAGGGTGAGTTTACTCTTGTGATCCTACGTGTATGGTCTCACATAACGAGATCGTTGTGGT
4257282 ATCTGGTAATGATGCAATGATAATTATTTTTTAATAATGTTGTCTTTATGACATGTTTTCTTATA
66 ATCTGGTAATGATGCAATGATAATTATTTTTTAATAATGTTGTCTTTATGACATGTTTTCTTATA
* *
4257347 -TTTTTTTATATGTTTCATCTATCTTTTGGTACGTTTTTTGTCATTTGATCGTTATTTTTGTTTA
131 TTTTTTTTATATGTTTCATCTATCTTTTGGTAAGTTTTTTGTCAATTGATCGTTATTTTTGTTTA
4257411 TAATTTTTATCATGGTTGGATTTGACATCGCAATCAAAATAGCGCTCGTTTGTTATAATGTTGAT
196 TAATTTTTATCATGGTTGGATTTGACATCGCAATCAAAATAGCGCTCGTTTGTTATAATGTTGAT
* * *
4257476 ATTCTCTACTTTGGACCCTCGGATTAGATTTGGATACGCAATTTCCATTTGTTGATATTTTTCTC
261 ATTCTCTACTTTGGACCCTCGGATTAGATTTGGATACGCAATTTCCATTTGTGGATAGTTTTATC
*
4257541 ACGTCGTTTGATCTTGATTTACGTTTTGTCGGCGGTCTTTCAATAGCTTGATCCTCTTTTGTGGT
326 ACGTCGCTTGATCTTGATTTACGTTTTGTCGGCGGTCTTTCAATAGCTTGATCCTCTTTTGTGGT
* * *
4257606 TCGTTTTGCCGATGCGGTCAGATATGTTCGTATCTACCTTTTAT
391 TCGTTTTGCCGATACGGCCAGATATGTTCGTATCTACCTTTGAT
4257650 TCA
1 TCA
4257653 AGTTTATTTG
Statistics
Matches: 419, Mismatches: 17, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
433 293 0.70
434 126 0.30
ACGTcount: A:0.20, C:0.14, G:0.19, T:0.46
Consensus pattern (434 bp):
TCATTAGGGTGAGTTTACTCTTGTGATCCTACGTGTATGGTCTCACATAACGAGATCGTTGTGGT
ATCTGGTAATGATGCAATGATAATTATTTTTTAATAATGTTGTCTTTATGACATGTTTTCTTATA
TTTTTTTTATATGTTTCATCTATCTTTTGGTAAGTTTTTTGTCAATTGATCGTTATTTTTGTTTA
TAATTTTTATCATGGTTGGATTTGACATCGCAATCAAAATAGCGCTCGTTTGTTATAATGTTGAT
ATTCTCTACTTTGGACCCTCGGATTAGATTTGGATACGCAATTTCCATTTGTGGATAGTTTTATC
ACGTCGCTTGATCTTGATTTACGTTTTGTCGGCGGTCTTTCAATAGCTTGATCCTCTTTTGTGGT
TCGTTTTGCCGATACGGCCAGATATGTTCGTATCTACCTTTGAT
Found at i:4259135 original size:29 final size:29
Alignment explanation
Indices: 4259090--4259147 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
4259080 TTGTTGGTCG
*
4259090 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
* *
4259119 TAGGTCGCCATGTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
4259148 AAGAGATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.14, C:0.36, G:0.28, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:4259283 original size:10 final size:10
Alignment explanation
Indices: 4259204--4259316 Score: 82
Period size: 10 Copynumber: 10.7 Consensus size: 10
4259194 GGCCATCTGA
*
4259204 CCGAGAGCAT
1 CCGAGGGCAT
*
4259214 CCGAGGCCAT
1 CCGAGGGCAT
*
4259224 CCGAGGCCAT
1 CCGAGGGCAT
*
4259234 CCGAGAGCAT
1 CCGAGGGCAT
*
4259244 CCGAGGCCAT
1 CCGAGGGCAT
*
4259254 CCGAACGAGCTAT
1 CCG-A-GGGC-AT
*
4259267 GCGAGGGCAT
1 CCGAGGGCAT
*
4259277 CCGAGGGCAA
1 CCGAGGGCAT
4259287 CCGAGCGAGCTAT
1 CCGAG-G-GC-AT
* *
4259300 GCGAGGGAAT
1 CCGAGGGCAT
4259310 CCGAGGG
1 CCGAGGG
4259317 AAGCCGAGCG
Statistics
Matches: 81, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
10 60 0.74
11 6 0.07
12 6 0.07
13 9 0.11
ACGTcount: A:0.25, C:0.30, G:0.35, T:0.10
Consensus pattern (10 bp):
CCGAGGGCAT
Found at i:4259316 original size:33 final size:33
Alignment explanation
Indices: 4259242--4259328 Score: 122
Period size: 33 Copynumber: 2.6 Consensus size: 33
4259232 ATCCGAGAGC
* * * *
4259242 ATCCGAGGCCATCCGAACGAGCTATGCGAGGGC
1 ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
4259275 ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
1 ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
4259308 ATCCGAGGG-AAGCCGAGCGAG
1 ATCCGAGGGCAA-CCGAGCGAG
4259329 GGTAGGTCGC
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 2 0.04
33 47 0.96
ACGTcount: A:0.26, C:0.26, G:0.38, T:0.09
Consensus pattern (33 bp):
ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
Found at i:4259378 original size:29 final size:29
Alignment explanation
Indices: 4259332--4259387 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
4259322 GAGCGAGGGT
*
4259332 AGGTCGCCCGGAGTGCATGGCAACCTACA
1 AGGTCGCCCGGAGGGCATGGCAACCTACA
*
4259361 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGGCAACCTA
4259388 TGTGTTGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.21, C:0.30, G:0.36, T:0.12
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCAACCTACA
Found at i:4259488 original size:29 final size:29
Alignment explanation
Indices: 4259446--4259502 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
4259436 GAGCAAGGGT
4259446 AGGTCGCCCAGAGTGCATGGCGACCTACA
1 AGGTCGCCCAGAGTGCATGGCGACCTACA
* *
4259475 AGGTCGTCCGGAGTGCATGGCGACCTAC
1 AGGTCGCCCAGAGTGCATGGCGACCTAC
4259503 GGCCAACACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.30, G:0.33, T:0.16
Consensus pattern (29 bp):
AGGTCGCCCAGAGTGCATGGCGACCTACA
Found at i:4260159 original size:21 final size:21
Alignment explanation
Indices: 4260119--4260159 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4260109 CACCAAACCT
***
4260119 AAATAAATTATTTCTTAAATG
1 AAATAAATTATTTAAAAAATG
4260140 AAATAAATTATTTAAAAAAT
1 AAATAAATTATTTAAAAAAT
4260160 AATAATCAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
AAATAAATTATTTAAAAAATG
Found at i:4265758 original size:21 final size:21
Alignment explanation
Indices: 4265717--4265758 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
4265707 GTCATACCAA
*
4265717 AGCTAAAACAGTGACGATAAG
1 AGCTAAAACAGTGAAGATAAG
*
4265738 AGCTAGAAAGAGTGAAG-TAAG
1 AGCTA-AAACAGTGAAGATAAG
4265759 TGCCACTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.48, C:0.10, G:0.29, T:0.14
Consensus pattern (21 bp):
AGCTAAAACAGTGAAGATAAG
Found at i:4267241 original size:29 final size:31
Alignment explanation
Indices: 4267208--4267267 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
4267198 AAAACGTGTC
*
4267208 ATAAAAATAAAAT-TATTAAAA-ATAAAAAA
1 ATAAAAATAAAATGTAATAAAATATAAAAAA
* *
4267237 ATAAAGATACAATGTAATAAAATATAAAAAA
1 ATAAAAATAAAATGTAATAAAATATAAAAAA
4267268 CAATGAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 11 0.42
30 7 0.27
31 8 0.31
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.23
Consensus pattern (31 bp):
ATAAAAATAAAATGTAATAAAATATAAAAAA
Found at i:4268675 original size:19 final size:19
Alignment explanation
Indices: 4268651--4268687 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4268641 ATAACCAACA
*
4268651 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
4268670 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
4268688 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:4268773 original size:21 final size:20
Alignment explanation
Indices: 4268713--4268775 Score: 56
Period size: 21 Copynumber: 3.1 Consensus size: 20
4268703 GTTTCCAGAT
**
4268713 TCACAACGCGATTT-GACTA
1 TCACAACGCGATTTAGAAAA
* * *
4268732 TCGCAACGCGATAATATAAAA
1 TCACAACGCGAT-TTAGAAAA
4268753 TCACAACGCGATTCTAGAAAA
1 TCACAACGCGATT-TAGAAAA
4268774 TC
1 TC
4268776 GCAATGCGAA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 11 0.33
20 1 0.03
21 21 0.64
ACGTcount: A:0.40, C:0.24, G:0.14, T:0.22
Consensus pattern (20 bp):
TCACAACGCGATTTAGAAAA
Found at i:4268784 original size:21 final size:21
Alignment explanation
Indices: 4268731--4268809 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
4268721 CGATTTGACT
* *
4268731 ATCGCAACGCGATAATATAAA
1 ATCGCAACGCGATTATACAAA
* * *
4268752 ATCACAACGCGATTCTAGAAA
1 ATCGCAACGCGATTATACAAA
*
4268773 ATCGCAATGCGAATTAATACAAA
1 ATCGCAACGCG-ATT-ATACAAA
* *
4268796 ATTGCAATGCGATT
1 ATCGCAACGCGATT
4268810 TTCCAAATTC
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
21 26 0.55
22 6 0.13
23 15 0.32
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.23
Consensus pattern (21 bp):
ATCGCAACGCGATTATACAAA
Found at i:4269281 original size:19 final size:19
Alignment explanation
Indices: 4269254--4269295 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
4269244 TATTTTGGAT
*
4269254 TTTTCACTATCGCAACACA
1 TTTTAACTATCGCAACACA
4269273 TTTTAACTATCGCAACACA
1 TTTTAACTATCGCAACACA
4269292 TTTT
1 TTTT
4269296 TCAAAATCGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.38
Consensus pattern (19 bp):
TTTTAACTATCGCAACACA
Found at i:4269304 original size:20 final size:20
Alignment explanation
Indices: 4269252--4269305 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
4269242 CTTATTTTGG
*
4269252 ATTTTTCACTATCGCAACAC
1 ATTTTTCAATATCGCAACAC
4269272 A-TTTT-AACTATCGCAACAC
1 ATTTTTCAA-TATCGCAACAC
*
4269291 ATTTTTCAAAATCGC
1 ATTTTTCAATATCGC
4269306 GTTGCGAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 1 0.03
19 16 0.55
20 10 0.34
21 2 0.07
ACGTcount: A:0.33, C:0.26, G:0.06, T:0.35
Consensus pattern (20 bp):
ATTTTTCAATATCGCAACAC
Found at i:4269322 original size:20 final size:20
Alignment explanation
Indices: 4269299--4269341 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
4269289 ACATTTTTCA
4269299 AAATCGCGTTGCGAATCTGG
1 AAATCGCGTTGCGAATCTGG
4269319 AAATCGCGTTGCGAATCTGG
1 AAATCGCGTTGCGAATCTGG
4269339 AAA
1 AAA
4269342 CTAAGTTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (20 bp):
AAATCGCGTTGCGAATCTGG
Found at i:4274020 original size:17 final size:17
Alignment explanation
Indices: 4273998--4274031 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
4273988 TATTGGCCGT
4273998 AGGTCGCCATGCACTCC
1 AGGTCGCCATGCACTCC
4274015 AGGTCGCCATGCACTCC
1 AGGTCGCCATGCACTCC
4274032 GGGCGACCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.41, G:0.24, T:0.18
Consensus pattern (17 bp):
AGGTCGCCATGCACTCC
Found at i:4274075 original size:12 final size:12
Alignment explanation
Indices: 4274058--4274082 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4274048 CTCAAACAGA
4274058 GAGAATGAACGT
1 GAGAATGAACGT
4274070 GAGAATGAACGT
1 GAGAATGAACGT
4274082 G
1 G
4274083 TTGCATAGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (12 bp):
GAGAATGAACGT
Found at i:4274144 original size:29 final size:28
Alignment explanation
Indices: 4274111--4274195 Score: 125
Period size: 29 Copynumber: 2.9 Consensus size: 28
4274101 TCCCAACACA
4274111 TAGGTCGCCATGTCCTCCGGGCGACCTTG
1 TAGGTCGCCATG-CCTCCGGGCGACCTTG
*
4274140 TAGGTCGCCATGCCCTCCGGGCGACATTG
1 TAGGTCGCCATG-CCTCCGGGCGACCTTG
*
4274169 TAGGTCGCCATGCACTCCGGGTGACCT
1 TAGGTCGCCATGC-CTCCGGGCGACCT
4274196 ACCCTCGCTC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 1 0.02
29 50 0.98
ACGTcount: A:0.13, C:0.34, G:0.31, T:0.22
Consensus pattern (28 bp):
TAGGTCGCCATGCCTCCGGGCGACCTTG
Found at i:4274243 original size:23 final size:23
Alignment explanation
Indices: 4274217--4274275 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
4274207 GCGGCTTCCT
*
4274217 TCGGATTCCCTCGCATAGCTCGC
1 TCGGATGCCCTCGCATAGCTCGC
* *
4274240 TCGGATGCCCTCGCATAGTTCGT
1 TCGGATGCCCTCGCATAGCTCGC
*
4274263 TCGGATGGCCTCG
1 TCGGATGCCCTCG
4274276 GTCGGATGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.12, C:0.34, G:0.27, T:0.27
Consensus pattern (23 bp):
TCGGATGCCCTCGCATAGCTCGC
Found at i:4274308 original size:34 final size:34
Alignment explanation
Indices: 4274263--4274328 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
4274253 CATAGTTCGT
*
4274263 TCGGATGGCCTCGGTCGGATGACCTCGGATGCTC
1 TCGGATAGCCTCGGTCGGATGACCTCGGATGCTC
4274297 TCGGATAGCCTCGGTCGGATGACCTCGGATGC
1 TCGGATAGCCTCGGTCGGATGACCTCGGATGC
4274329 CCAGCGTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.14, C:0.29, G:0.35, T:0.23
Consensus pattern (34 bp):
TCGGATAGCCTCGGTCGGATGACCTCGGATGCTC
Found at i:4275104 original size:5 final size:5
Alignment explanation
Indices: 4275091--4275127 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
4275081 CAATGAGTTG
* *
4275091 AAATA AAATG AAATA AAATG AAATA AAATA AAATA AA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AA
4275128 CCCTCAAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:4275104 original size:10 final size:10
Alignment explanation
Indices: 4275089--4275127 Score: 69
Period size: 10 Copynumber: 3.9 Consensus size: 10
4275079 TCCAATGAGT
4275089 TGAAATAAAA
1 TGAAATAAAA
4275099 TGAAATAAAA
1 TGAAATAAAA
4275109 TGAAATAAAA
1 TGAAATAAAA
*
4275119 TAAAATAAA
1 TGAAATAAA
4275128 CCCTCAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.21
Consensus pattern (10 bp):
TGAAATAAAA
Found at i:4279277 original size:168 final size:167
Alignment explanation
Indices: 4279001--4279335 Score: 645
Period size: 168 Copynumber: 2.0 Consensus size: 167
4278991 GCAATTATCA
4279001 TATTGACATGTCTTTATTTTGTTGATATATATAATTGCTCTTTGGTCTCTCGTTTAGAATGTTCC
1 TATTGACATGTCTTTATTTTGTTGATATATATAATTGCTCTTTGGTCTCTCGTTTAGAATGTTCC
4279066 TCCAGCAATCCTCCTTCGTTTCCTACGGGAACACAGATCAGAATGGGCTGACTGCGGCATTGATG
66 TCCAGCAATCCTCCTTCGTTTCCTACGGGAACACAGATCAGAATGGGCTGACTGCGGCATTGATG
4279131 CTTACTCAGCTGCGGTTG-TAAAGTTGGTCCCTGTAG
131 CTTACTCAGCTGCGGTTGTTAAAGTTGGTCCCTGTAG
4279167 TATTGACATGTCTTTATTTTGTTGATATATATATATTTGCTCTTTGGTCTCTCGTTTAGAATGTT
1 TATTGACATGTCTTTATTTTGTTGATATATATA-A-TTGCTCTTTGGTCTCTCGTTTAGAATGTT
4279232 CCTCCAGCAATCCTCCTTCGTTTCCTACGGGAACACAGATCAGAATGGGCTGACTGCGGCATTGA
64 CCTCCAGCAATCCTCCTTCGTTTCCTACGGGAACACAGATCAGAATGGGCTGACTGCGGCATTGA
4279297 TGCTTACTCAGCTGCGGTTGTTAAAGTTGGTCCCTGTAG
129 TGCTTACTCAGCTGCGGTTGTTAAAGTTGGTCCCTGTAG
4279336 CCTACGAGGA
Statistics
Matches: 166, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
166 33 0.20
167 1 0.01
168 114 0.69
169 18 0.11
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.37
Consensus pattern (167 bp):
TATTGACATGTCTTTATTTTGTTGATATATATAATTGCTCTTTGGTCTCTCGTTTAGAATGTTCC
TCCAGCAATCCTCCTTCGTTTCCTACGGGAACACAGATCAGAATGGGCTGACTGCGGCATTGATG
CTTACTCAGCTGCGGTTGTTAAAGTTGGTCCCTGTAG
Found at i:4284016 original size:25 final size:25
Alignment explanation
Indices: 4283988--4284035 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
4283978 ATAACTCTTT
4283988 TATA-AAAATATATTTATAAAAATTG
1 TATATAAAATATA-TTATAAAAATTG
* *
4284013 TATATAAAATCTATTGTAAAAAT
1 TATATAAAATATATTATAAAAAT
4284036 AATTAGTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (25 bp):
TATATAAAATATATTATAAAAATTG
Found at i:4285593 original size:19 final size:18
Alignment explanation
Indices: 4285542--4285593 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 18
4285532 TAACAAGTTG
*
4285542 AAAATATTTATATTCTTTAA
1 AAAATA-TTATATT-TATAA
*
4285562 AAAA-ATTAAATTTATAA
1 AAAATATTATATTTATAA
4285579 AAAATATATATATTT
1 AAAATAT-TATATTT
4285594 TTTACAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
17 8 0.30
18 8 0.30
19 7 0.26
20 4 0.15
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
AAAATATTATATTTATAA
Found at i:4285614 original size:36 final size:37
Alignment explanation
Indices: 4285542--4285617 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 37
4285532 TAACAAGTTG
* **
4285542 AAAATATTTATATTCTTTAAAAAAATTAAATTTATAA
1 AAAATATATATATTCTTTAAAAAAATTAAAAATATAA
* *
4285579 AAAATATATATATT-TTTTACAAAATTAAAAATATAA
1 AAAATATATATATTCTTTAAAAAAATTAAAAATATAA
4285615 AAA
1 AAA
4285618 GGTTTAATGA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 21 0.62
37 13 0.38
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (37 bp):
AAAATATATATATTCTTTAAAAAAATTAAAAATATAA
Found at i:4287027 original size:25 final size:24
Alignment explanation
Indices: 4286999--4287045 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
4286989 AAAAAATATT
*
4286999 TTAACTATCTATTTTAATAAAAAAA
1 TTAAATATCTA-TTTAATAAAAAAA
* *
4287024 TTAAATGTTTATTTAATAAAAA
1 TTAAATATCTATTTAATAAAAA
4287046 TACTTTAAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (24 bp):
TTAAATATCTATTTAATAAAAAAA
Found at i:4292356 original size:37 final size:38
Alignment explanation
Indices: 4292306--4292380 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
4292296 CTGTCGATAT
4292306 CTTTACATAATCC-TTTCTTCAAAAGAAATCATGTTAA
1 CTTTACATAATCCTTTTCTTCAAAAGAAATCATGTTAA
4292343 CTTTACATAATCCTTTTCTTCAAAAGAAATCATGTTAA
1 CTTTACATAATCCTTTTCTTCAAAAGAAATCATGTTAA
4292381 ACAATCAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 13 0.35
38 24 0.65
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.39
Consensus pattern (38 bp):
CTTTACATAATCCTTTTCTTCAAAAGAAATCATGTTAA
Found at i:4294200 original size:2 final size:2
Alignment explanation
Indices: 4294193--4294235 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
4294183 ACCGCGAATG
4294193 TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4294233 TA T
1 TA T
4294236 TTTGTATTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:4294219 original size:21 final size:21
Alignment explanation
Indices: 4294193--4294235 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
4294183 ACCGCGAATG
4294193 TATATATATATATATATTATA
1 TATATATATATATATATTATA
4294214 TATATATATATATATATTATA
1 TATATATATATATATATTATA
4294235 T
1 T
4294236 TTTGTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TATATATATATATATATTATA
Found at i:4300803 original size:20 final size:20
Alignment explanation
Indices: 4300778--4300870 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
4300768 TTTTCCCAAT
4300778 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
4300798 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
4300818 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
4300839 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
4300860 TCGCAATGCGA
1 TCGCAATGCGA
4300871 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:4300820 original size:41 final size:41
Alignment explanation
Indices: 4300775--4300870 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
4300765 CGATTTTCCC
4300775 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
4300816 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
4300857 AAATCGCAATGCGA
1 AATTCGCAATGCGA
4300871 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:4300824 original size:21 final size:20
Alignment explanation
Indices: 4300778--4300870 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
4300768 TTTTCCCAAT
*
4300778 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
4300798 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
4300818 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
4300839 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
4300860 TCGCAATGCGA
1 TCGCAATGCGA
4300871 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:4300884 original size:20 final size:20
Alignment explanation
Indices: 4300859--4300952 Score: 64
Period size: 20 Copynumber: 4.7 Consensus size: 20
4300849 AATTGGGAAA
4300859 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * * **
4300879 ATCGCAATACGATAATAAAAA
1 ATCGCAATGCGATACT-GACT
* *
4300900 ATCGCAACT-AGATACTTACT
1 ATCGCAA-TGCGATACTGACT
* *
4300920 TTCGCAACGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
4300940 TTCGCAACGCGAT
1 ATCGCAATGCGAT
4300953 TTACATAGCG
Statistics
Matches: 57, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
20 43 0.75
21 13 0.23
22 1 0.02
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:4300933 original size:41 final size:41
Alignment explanation
Indices: 4300856--4300933 Score: 95
Period size: 41 Copynumber: 1.9 Consensus size: 41
4300846 GCGAATTGGG
* *
4300856 AAAATCGCAATGCGATACTGACTATCGCAATACGATAATAA
1 AAAATCGCAATGAGATACTGACTATCGCAACACGATAATAA
* * *
4300897 AAAATCGCAACT-AGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAA-TGAGATACTGACTATCGCAACACGATA
4300934 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 30 0.97
42 1 0.03
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.23
Consensus pattern (41 bp):
AAAATCGCAATGAGATACTGACTATCGCAACACGATAATAA
Found at i:4301549 original size:19 final size:19
Alignment explanation
Indices: 4301527--4301616 Score: 153
Period size: 19 Copynumber: 4.7 Consensus size: 19
4301517 GAAACCAAAA
*
4301527 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
4301546 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
4301565 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
4301584 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
4301604 TCGCGTTGCGATT
1 TCGCGTTGCGATT
4301617 GTCTGGTAGC
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
19 49 0.73
20 18 0.27
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:4301604 original size:39 final size:38
Alignment explanation
Indices: 4301527--4301616 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
4301517 GAAACCAAAA
*
4301527 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
4301565 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
4301604 TCGCGTTGCGATT
1 TCGCGTTGCGATT
4301617 GTCTGGTAGC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 21 0.43
39 28 0.57
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:4301636 original size:33 final size:33
Alignment explanation
Indices: 4301599--4301683 Score: 125
Period size: 33 Copynumber: 2.5 Consensus size: 33
4301589 GTTGCGATTT
* *
4301599 TCATTTCGCGTTGCGATTGTCTGGTAGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTAGCGATAG
* *
4301632 TCATTTCGCGTTGCAATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTAGCGATAG
4301665 TCATTTCCGCGTTGCGATT
1 TCATTT-CGCGTTGCGATT
4301684 TTCATTTCAA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 35 0.76
34 11 0.24
ACGTcount: A:0.14, C:0.22, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTAGCGATAG
Found at i:4303770 original size:21 final size:21
Alignment explanation
Indices: 4303746--4303812 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
4303736 TCATTCCTCG
4303746 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
4303767 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
4303788 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
4303809 AGAG
1 AGAG
4303813 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:4303770 original size:42 final size:42
Alignment explanation
Indices: 4303690--4303812 Score: 106
Period size: 42 Copynumber: 2.9 Consensus size: 42
4303680 GCCCGACTCG
* * * * * * *
4303690 CCTATCATCCCTCAAGATTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
4303732 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
* * * * *
4303774 ACTGTCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTATCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
4303813 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 61 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.37, G:0.17, T:0.24
Consensus pattern (42 bp):
CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
Found at i:4305188 original size:14 final size:14
Alignment explanation
Indices: 4305169--4305204 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
4305159 ATTGTTTAAT
4305169 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
4305183 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
4305197 TGATTTGT
1 TGATTTGT
4305205 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:4305374 original size:19 final size:20
Alignment explanation
Indices: 4305352--4305394 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
4305342 GAATCGCAAC
*
4305352 GCGAAATTAAATT-CGCGTT
1 GCGAAAGTAAATTCCGCGTT
* *
4305371 GCGATAGTAACTTCCGCGTT
1 GCGAAAGTAAATTCCGCGTT
4305391 GCGA
1 GCGA
4305395 TGGACATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (20 bp):
GCGAAAGTAAATTCCGCGTT
Found at i:4307684 original size:12 final size:12
Alignment explanation
Indices: 4307667--4307691 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4307657 TCTTCGGGGA
4307667 CTTTTTCTTCTT
1 CTTTTTCTTCTT
4307679 CTTTTTCTTCTT
1 CTTTTTCTTCTT
4307691 C
1 C
4307692 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:4307900 original size:24 final size:24
Alignment explanation
Indices: 4307866--4307919 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
4307856 CTGAAACATC
* *
4307866 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
4307890 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
4307914 ATCAAA
1 ATCAAA
4307920 TTTCGAATAC
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:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:4309004 original size:20 final size:20
Alignment explanation
Indices: 4308979--4309076 Score: 169
Period size: 20 Copynumber: 4.9 Consensus size: 20
4308969 ATTCATTTGA
4308979 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
4308999 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
4309019 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
4309039 CTATTGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
4309059 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
4309077 CGCAATGCGA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 74 1.00
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:4309136 original size:19 final size:19
Alignment explanation
Indices: 4309114--4309181 Score: 136
Period size: 19 Copynumber: 3.6 Consensus size: 19
4309104 GATTTTCTCG
4309114 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4309133 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4309152 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4309171 TTGCGATTTTC
1 TTGCGATTTTC
4309182 TCGTTGCGAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.15, C:0.21, G:0.16, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:4309199 original size:33 final size:33
Alignment explanation
Indices: 4309095--4309210 Score: 142
Period size: 33 Copynumber: 3.4 Consensus size: 33
4309085 GAAATGAAAA
*
4309095 TCGCATTGAGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
4309128 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTC---TCG--TTGCGATTTTCATT
***
4309166 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
*
4309199 TCGCGTTGCGAT
1 TCGCATTGCGAT
4309211 AGTCTGTTTT
Statistics
Matches: 73, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
33 37 0.51
35 3 0.04
36 3 0.04
38 30 0.41
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.44
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
Found at i:4311177 original size:19 final size:19
Alignment explanation
Indices: 4311153--4311219 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
4311143 GAAACTTAAA
4311153 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
* *
4311172 ATCGCAACGTGGAAATGGCT
1 ATCGCAACG-CGAAATGACT
* **
4311192 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
4311211 ATCGCAACG
1 ATCGCAACG
4311220 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 23 0.59
20 16 0.41
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:4311227 original size:14 final size:14
Alignment explanation
Indices: 4311208--4311265 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
4311198 ATGCGAAATG
4311208 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
4311222 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
4311238 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
4311254 AAAATCGCAACG
1 AAAATCGCAACG
4311266 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:4311250 original size:32 final size:33
Alignment explanation
Indices: 4311192--4311270 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
4311182 GGAAATGGCT
*
4311192 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
4311225 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
4311257 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
4311271 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:4311299 original size:19 final size:16
Alignment explanation
Indices: 4311277--4311372 Score: 56
Period size: 19 Copynumber: 5.7 Consensus size: 16
4311267 GAAACACAAA
4311277 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTT-ATT
*
4311296 TCGCGTTGCGATTT-TG
1 TCGC-TTGCGATTTATT
4311312 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTT-ATT
* *
4311328 TTGCGTTGCGATTT-TG
1 TCGC-TTGCGATTTATT
4311344 TCG-TTGCGATTTTTATT
1 TCGCTTGCGA--TTTATT
4311361 TCGCATTGCGAT
1 TCGC-TTGCGAT
4311373 AGCCATTTCC
Statistics
Matches: 61, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
14 15 0.25
16 13 0.21
17 5 0.08
18 12 0.20
19 16 0.26
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (16 bp):
TCGCTTGCGATTTATT
Found at i:4311318 original size:14 final size:14
Alignment explanation
Indices: 4311299--4311356 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
4311289 TTTCATTTCG
4311299 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
4311313 CGTTGCGATTTCATTTT
1 CGTTGCGA-TT--TTGT
4311330 GCGTTGCGATTTTGT
1 -CGTTGCGATTTTGT
4311345 CGTTGCGATTTT
1 CGTTGCGATTTT
4311357 TATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 20 0.53
15 5 0.13
17 5 0.13
18 8 0.21
ACGTcount: A:0.09, C:0.16, G:0.26, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:4311334 original size:32 final size:32
Alignment explanation
Indices: 4311282--4311372 Score: 137
Period size: 32 Copynumber: 2.8 Consensus size: 32
4311272 ACAAATCGCA
4311282 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
*
4311315 TTGCGATTTCATTTTGCGTTGCGATTTTGTCG
1 TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
* *
4311347 TTGCGATTTTTATTTCGCATTGCGAT
1 TTGCGA-TTTCATTTCGCGTTGCGAT
4311373 AGCCATTTCC
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 31 0.58
33 22 0.42
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.49
Consensus pattern (32 bp):
TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
Found at i:4311380 original size:19 final size:20
Alignment explanation
Indices: 4311358--4311400 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
4311348 TGCGATTTTT
4311358 ATTT-CGCATTGCGATAGCC
1 ATTTCCGCATTGCGATAGCC
* *
4311377 ATTTCCGCGTTGCGATAGTC
1 ATTTCCGCATTGCGATAGCC
4311397 ATTT
1 ATTT
4311401 TCGTGTTGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (20 bp):
ATTTCCGCATTGCGATAGCC
Found at i:4311909 original size:18 final size:18
Alignment explanation
Indices: 4311883--4311927 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
4311873 GTCGATCAGA
*
4311883 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
4311901 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
4311919 TGATGGCTC
1 TGATGGCTC
4311928 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:4313272 original size:20 final size:20
Alignment explanation
Indices: 4313247--4313284 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4313237 AATAATTTCT
4313247 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
4313267 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
4313285 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:4313573 original size:22 final size:22
Alignment explanation
Indices: 4313548--4313591 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
4313538 GATTTAGATA
4313548 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
4313570 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
4313592 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:4313804 original size:20 final size:20
Alignment explanation
Indices: 4313779--4313872 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
4313769 GATTATGTAT
4313779 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
4313799 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
4313819 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
4313840 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
4313860 TATCGCATTGCGA
1 TATCGCGTTGCGA
4313873 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:4313873 original size:20 final size:20
Alignment explanation
Indices: 4313759--4313873 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
4313749 CGCTTTGAAA
*
4313759 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
4313780 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
4313800 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
4313820 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
4313841 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
4313861 ATCGCATTGCGAT
1 ATCGCATTGCGAT
4313874 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:4313892 original size:41 final size:41
Alignment explanation
Indices: 4313801--4313935 Score: 121
Period size: 41 Copynumber: 3.3 Consensus size: 41
4313791 AAAGTCAGTA
* * * ** *
4313801 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
4313841 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
4313883 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
*
4313924 TCACGTTGCGAT
1 TCGCGTTGCGAT
4313936 TTACTTATTC
Statistics
Matches: 77, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
40 3 0.04
41 72 0.94
42 2 0.03
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:4313906 original size:20 final size:20
Alignment explanation
Indices: 4313862--4313954 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
4313852 ATAGTCAGTA
* **
4313862 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
4313883 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
4313903 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
* *
4313924 TCACGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
4313944 TCGCATTGCGA
1 TCGCATTGCGA
4313955 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:4313936 original size:41 final size:41
Alignment explanation
Indices: 4313862--4313957 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
4313852 ATAGTCAGTA
* *
4313862 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCACGTTGCGATTTACTTAT
4313903 TCGCATTGCGAATTTCCCAATTCACGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCACGTTGCGATTTACTTAT
4313944 TCGCATTGCGAATT
1 TCGCATTGCGAATT
4313958 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCACGTTGCGATTTACTTAT
Found at i:4314484 original size:17 final size:18
Alignment explanation
Indices: 4314447--4314491 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
4314437 TGAAGTAGAT
*
4314447 AATATTTAAAAAAAATAA
1 AATAATTAAAAAAAATAA
*
4314465 AATAATTAAAAATAAT-A
1 AATAATTAAAAAAAATAA
4314482 AATAA-TAAAA
1 AATAATTAAAA
4314492 TATTTGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 5 0.20
17 6 0.24
18 14 0.56
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
AATAATTAAAAAAAATAA
Found at i:4319858 original size:3 final size:3
Alignment explanation
Indices: 4319850--4319879 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
4319840 GTGACATTAC
4319850 ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
4319880 ATATATACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:4319938 original size:19 final size:20
Alignment explanation
Indices: 4319910--4319951 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
4319900 AATTAAATTT
*
4319910 AAAATGATA-CACAAATCCA
1 AAAATGATACCACAAACCCA
*
4319929 AAAATTATACCACAAACCCA
1 AAAATGATACCACAAACCCA
4319949 AAA
1 AAA
4319952 TCACAAACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.60, C:0.24, G:0.02, T:0.14
Consensus pattern (20 bp):
AAAATGATACCACAAACCCA
Found at i:4325368 original size:12 final size:12
Alignment explanation
Indices: 4325351--4325375 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4325341 CGCTTTGCTC
4325351 CTAAACCATCCG
1 CTAAACCATCCG
4325363 CTAAACCATCCG
1 CTAAACCATCCG
4325375 C
1 C
4325376 CCGGTTGCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.44, G:0.08, T:0.16
Consensus pattern (12 bp):
CTAAACCATCCG
Found at i:4327703 original size:3 final size:3
Alignment explanation
Indices: 4327695--4327729 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
4327685 TTTTACGTTA
4327695 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4327730 ATGTAATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4330400 original size:23 final size:23
Alignment explanation
Indices: 4330370--4330414 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
4330360 AACTTTTGGC
4330370 TTCTGGTTATATTTGCTCCAATA
1 TTCTGGTTATATTTGCTCCAATA
4330393 TTCTGGTTATATTTGCTCCAAT
1 TTCTGGTTATATTTGCTCCAAT
4330415 TTTGTTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.20, C:0.18, G:0.13, T:0.49
Consensus pattern (23 bp):
TTCTGGTTATATTTGCTCCAATA
Found at i:4338921 original size:60 final size:59
Alignment explanation
Indices: 4338818--4338982 Score: 192
Period size: 60 Copynumber: 2.8 Consensus size: 59
4338808 TTTGGATGTA
* ** *
4338818 TTTAGGGATGAAGTTAGAATATTCAAAAGTTTGGGGACCAATTTAGAA-AGAAGGTCATAG
1 TTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAAGAGAA--TCATAG
* * *
4338878 TTTAGGGATGAAATTAGAATGTTCAAAAGTTTAAGGACTAATTTATAATGAGAATTATAG
1 TTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAA-GAGAATCATAG
*
4338938 TTT-GGAGATGAAATT-GAAATATTCAAAAGTTTAAAGACTAATTTA
1 TTTAGG-GATGAAATTAG-AATATTCAAAAGTTTAAGGACTAATTTA
4338983 AAATTAGAGT
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
59 3 0.03
60 85 0.92
62 4 0.04
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.33
Consensus pattern (59 bp):
TTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAAGAGAATCATAG
Found at i:4338996 original size:60 final size:60
Alignment explanation
Indices: 4338824--4339005 Score: 174
Period size: 60 Copynumber: 3.0 Consensus size: 60
4338814 TGTATTTAGG
* *** * * *
4338824 GATGAAGTTAGAATATTCAAAAGTTTGGGGACCAATTTAGAAA-GA-AGGTCATAGTTTAGG-
1 GATGAAATTAGAATATTCAAAAGTTTAAAGACTAATTTA-AAATGAGA-ATTATAGTTT-GGA
* * *
4338884 GATGAAATTAGAATGTTCAAAAGTTTAAGGACTAATTTATAATGAGAATTATAGTTTGGA
1 GATGAAATTAGAATATTCAAAAGTTTAAAGACTAATTTAAAATGAGAATTATAGTTTGGA
* * * *
4338944 GATGAAATT-GAAATATTCAAAAGTTTAAAGACTAATTTAAAATTAGAGTTATAATTTAGA
1 GATGAAATTAG-AATATTCAAAAGTTTAAAGACTAATTTAAAATGAGAATTATAGTTTGGA
4339004 GA
1 GA
4339006 CATGTGATGT
Statistics
Matches: 103, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
59 5 0.05
60 97 0.94
61 1 0.01
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.32
Consensus pattern (60 bp):
GATGAAATTAGAATATTCAAAAGTTTAAAGACTAATTTAAAATGAGAATTATAGTTTGGA
Found at i:4345995 original size:54 final size:54
Alignment explanation
Indices: 4345837--4345978 Score: 221
Period size: 54 Copynumber: 2.6 Consensus size: 54
4345827 TCTTTTACAG
* * ** *
4345837 TAGCTCGGGATGGATAAATCGTGCCCACGCCTTAACTGAAGACTTCTTTTGCGT
1 TAGCTCTGGATGAATAAGCCGTGCCCACGCCTTAACTGAAGACTTCTTCTGCGT
* *
4345891 TAGTTCTGGATGAATAAGCCGTGCCCAAGCCTTAACTGAAGACTTCTTCTGCGT
1 TAGCTCTGGATGAATAAGCCGTGCCCACGCCTTAACTGAAGACTTCTTCTGCGT
4345945 TAGCTCTGGATGAATAAGCCGTGCCCACGCCTTA
1 TAGCTCTGGATGAATAAGCCGTGCCCACGCCTTA
4345979 TGCGAACGCC
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 79 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.28
Consensus pattern (54 bp):
TAGCTCTGGATGAATAAGCCGTGCCCACGCCTTAACTGAAGACTTCTTCTGCGT
Found at i:4347193 original size:45 final size:45
Alignment explanation
Indices: 4347123--4347209 Score: 122
Period size: 45 Copynumber: 1.9 Consensus size: 45
4347113 ATACACGACA
* *
4347123 ATAGTATAGACAAATTTTGAGACTAATA-CAGCAAACATTATTTTC
1 ATAGTATAGACAAATTCTGAAACTAATACCA-CAAACATTATTTTC
* *
4347168 ATAGTCTAGATAAATTCTGAAACTAATACCACAAACATTATT
1 ATAGTATAGACAAATTCTGAAACTAATACCACAAACATTATT
4347210 GTCGTTACTA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 35 0.95
46 2 0.05
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (45 bp):
ATAGTATAGACAAATTCTGAAACTAATACCACAAACATTATTTTC
Found at i:4349372 original size:18 final size:18
Alignment explanation
Indices: 4349349--4349386 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
4349339 AAAGAAAATG
4349349 ATATCCAGTAAAGAGTTA
1 ATATCCAGTAAAGAGTTA
4349367 ATATCCAGTAAAGAGTTA
1 ATATCCAGTAAAGAGTTA
4349385 AT
1 AT
4349387 TAATGGAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.29
Consensus pattern (18 bp):
ATATCCAGTAAAGAGTTA
Found at i:4354466 original size:2 final size:2
Alignment explanation
Indices: 4354459--4354502 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
4354449 TCGATCTACA
4354459 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4354500 AT A
1 AT A
4354503 ATTTCCGAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4354833 original size:84 final size:83
Alignment explanation
Indices: 4354557--4354843 Score: 369
Period size: 84 Copynumber: 3.5 Consensus size: 83
4354547 TAATGATGTT
*
4354557 GCTTC-ATGACACGC-ATGTAAGTCATATATGCGTGTCATAAATTTATGA-CACACAATGT-TGT
1 GCTTCAATGACACGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACCACA-AATGTGTGT
*
4354618 CAAGC--AGA-TTATGACGGG
65 C-ATCTTA-ATTTATGACGGG
* * * *
4354636 GCTTCAATGACGCGTAA-GTAAGTTATACATACGTGTCAT-AATTTATGACCACAAATGTGTGTC
1 GCTTCAATGACACGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACCACAAATGTGTGTC
*
4354699 ATCTTAATTTATGACGGT
66 ATCTTAATTTATGACGGG
*
4354717 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTC-TAAATTTATGACGCACAAATGTGTGT
1 GCTTCAATGACACGCAATGTAAGTCATACATGCGTGTCATAAATTTATGAC-CACAAATGTGTGT
4354781 CATCTTAATTTATGACGGGG
65 CATCTTAATTTATGAC-GGG
* *
4354801 GCTTCAATGACACGCAATGTATGTCATACATGCGCGTCATAAA
1 GCTTCAATGACACGCAATGTAAGTCATACATGCGTGTCATAAA
4354844 AAATTCATGT
Statistics
Matches: 182, Mismatches: 14, Indels: 18
0.85 0.07 0.08
Matches are distributed among these distances:
79 21 0.12
80 35 0.19
81 28 0.15
82 28 0.15
83 29 0.16
84 37 0.20
85 4 0.02
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Consensus pattern (83 bp):
GCTTCAATGACACGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACCACAAATGTGTGTC
ATCTTAATTTATGACGGG
Found at i:4355963 original size:14 final size:15
Alignment explanation
Indices: 4355932--4355964 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4355922 AAAAGTAAGT
4355932 TAAAACATAAATCAA
1 TAAAACATAAATCAA
*
4355947 TAAAATATAAA-CAA
1 TAAAACATAAATCAA
4355961 TAAA
1 TAAA
4355965 CAATAACTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (15 bp):
TAAAACATAAATCAA
Found at i:4356538 original size:18 final size:17
Alignment explanation
Indices: 4356481--4356571 Score: 85
Period size: 17 Copynumber: 5.2 Consensus size: 17
4356471 AATCTATGCA
4356481 TGATAACTGTAAAA-ATC
1 TGATAACTG-AAAACATC
*
4356498 TGATAACTGTAAACATC
1 TGATAACTGAAAACATC
*
4356515 TGATAACTGAAAATCATT
1 TGATAACTGAAAA-CATC
* *
4356533 TGATAACTAAAAATCATA
1 TGATAACTGAAAA-CATC
* * *
4356551 TGATAATTGTAAATATC
1 TGATAACTGAAAACATC
4356568 TGAT
1 TGAT
4356572 GTCCACTTGT
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
16 3 0.05
17 30 0.48
18 29 0.47
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (17 bp):
TGATAACTGAAAACATC
Found at i:4365301 original size:22 final size:22
Alignment explanation
Indices: 4365275--4365337 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
4365265 TTCACTCTGT
4365275 CAACCAAATAGAAAACTATCAAG
1 CAACCAAATAGAAAACTATC-AG
* * *
4365298 -AACCATATATGTAAAC-AACAG
1 CAACCAAATA-GAAAACTATCAG
*
4365319 CAACCAAAGAGAAAACTAT
1 CAACCAAATAGAAAACTAT
4365338 TATATAATAG
Statistics
Matches: 30, Mismatches: 7, Indels: 7
0.68 0.16 0.16
Matches are distributed among these distances:
21 7 0.23
22 18 0.60
23 5 0.17
ACGTcount: A:0.56, C:0.21, G:0.10, T:0.14
Consensus pattern (22 bp):
CAACCAAATAGAAAACTATCAG
Found at i:4395064 original size:31 final size:31
Alignment explanation
Indices: 4395026--4395097 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
4395016 GGATTAAGAT
4395026 TCAAATTGGTACATAAACTTGGCTTCATGGA
1 TCAAATTGGTACATAAACTTGGCTTCATGGA
* * * * *
4395057 TCAAATTGCTACCTGAACTTGTCTTCTTGGA
1 TCAAATTGGTACATAAACTTGGCTTCATGGA
4395088 TCAAATTGGT
1 TCAAATTGGT
4395098 TAAAAAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (31 bp):
TCAAATTGGTACATAAACTTGGCTTCATGGA
Found at i:4400407 original size:24 final size:22
Alignment explanation
Indices: 4400358--4400403 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
4400348 AAAAAGATAT
*
4400358 ATATAAATAAATTTATATGTTG
1 ATATAAATAAATTTATATGTTA
*
4400380 ATATAAATAAATTTTTAT-TTA
1 ATATAAATAAATTTATATGTTA
4400401 ATA
1 ATA
4400404 ATATTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (22 bp):
ATATAAATAAATTTATATGTTA
Found at i:4401774 original size:41 final size:43
Alignment explanation
Indices: 4401728--4401814 Score: 108
Period size: 40 Copynumber: 2.1 Consensus size: 43
4401718 TGTTTATACA
* * *
4401728 AAAAAAATGTCGCTATTGATT-ATACTATAGTGGCGTTTGT-T
1 AAAAAAATGCCACTATTGATTAAAACTATAGTGGCGTTTGTCT
* *
4401769 -AAAAAATGCCACTATTGATTAAAACTATTGTGGTGTTTGTCT
1 AAAAAAATGCCACTATTGATTAAAACTATAGTGGCGTTTGTCT
4401811 AAAA
1 AAAA
4401815 GCGCCACTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
40 18 0.47
41 16 0.42
42 1 0.03
43 3 0.08
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (43 bp):
AAAAAAATGCCACTATTGATTAAAACTATAGTGGCGTTTGTCT
Found at i:4401784 original size:40 final size:40
Alignment explanation
Indices: 4401729--4401891 Score: 127
Period size: 41 Copynumber: 4.0 Consensus size: 40
4401719 GTTTATACAA
* * *
4401729 AAAAAATGTCGCTATTGATTATACTATAGTGGCGTTTGTT
1 AAAAAATGCCACTATTGATTATACTATTGTGGCGTTTGTT
* *
4401769 AAAAAATGCCACTATTGATTAAAACTATTGTGGTGTTTGTCT
1 AAAAAATGCCACTATTGATT-ATACTATTGTGGCGTTTGT-T
** * * *
4401811 -AAAAGCGCCACTATTTATTATCACTATTGCGGCGTTT-TA
1 AAAAAATGCCACTATTGATTAT-ACTATTGTGGCGTTTGTT
*
4401850 AGAATAAATGCCACTATATG-TGTA-ATCTATTGCGGCGTTTGT
1 A-AA-AAATGCCACTAT-TGAT-TATA-CTATTGTGGCGTTTGT
4401892 GGTATAAACG
Statistics
Matches: 98, Mismatches: 15, Indels: 17
0.75 0.12 0.13
Matches are distributed among these distances:
40 20 0.20
41 48 0.49
42 26 0.27
43 4 0.04
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.37
Consensus pattern (40 bp):
AAAAAATGCCACTATTGATTATACTATTGTGGCGTTTGTT
Found at i:4401919 original size:42 final size:42
Alignment explanation
Indices: 4401873--4402008 Score: 157
Period size: 42 Copynumber: 3.2 Consensus size: 42
4401863 CTATATGTGT
*
4401873 AATCTATTGCGGCGTTTGTGGTATAAACGCCGCTAATTTACC
1 AATCTATTGCGGCGTTTATGGTATAAACGCCGCTAATTTACC
* * * *
4401915 AATCTGTTGCAGCGTTTATGGTTTAAACGCTGCTAATTTACC
1 AATCTATTGCGGCGTTTATGGTATAAACGCCGCTAATTTACC
* * * * * *
4401957 ACTCTATTGCGGCGTTTTTTGTAAAAACGCCGCTATATGT-CA
1 AATCTATTGCGGCGTTTATGGTATAAACGCCGCTA-ATTTACC
4401999 AATCTATTGC
1 AATCTATTGC
4402009 AGCGAAGTAA
Statistics
Matches: 77, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
42 74 0.96
43 3 0.04
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (42 bp):
AATCTATTGCGGCGTTTATGGTATAAACGCCGCTAATTTACC
Found at i:4403376 original size:20 final size:20
Alignment explanation
Indices: 4403351--4403388 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
4403341 TTTGGTTCAC
4403351 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
4403371 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
4403389 GGAATAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:4409262 original size:20 final size:21
Alignment explanation
Indices: 4409219--4409262 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4409209 TTAATAAAAA
* *
4409219 TTATTTAAAATATTATTATTT
1 TTATTTAAAATATCAATATTT
4409240 TTATTTAAAATATCAAT-TTT
1 TTATTTAAAATATCAATATTT
4409260 TTA
1 TTA
4409263 ATATTTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATTTAAAATATCAATATTT
Found at i:4410126 original size:111 final size:111
Alignment explanation
Indices: 4409995--4410455 Score: 708
Period size: 111 Copynumber: 4.1 Consensus size: 111
4409985 TTGTCGGTTT
* * * *
4409995 GTGTCGATACTTTATAAAAAAATAT-TATTCTATAATAATATAACAGGTAAAAAAATGACAAAAT
1 GTGTCGATACTTTATAAAAATATATCGA-TCTATAACAATATAACAGGT-AAAAAATGACAAAAC
4410059 CGGTCTATAAATGACAAAACAGGTAAAGCGCTATCGAATATATTGAAA
64 CGGTCTATAAATGACAAAACAGGTAAAGCGCTATCGAATATATTGAAA
*
4410107 GTGTCGATACTTTATAAAAATGTATCGATCTATAACAATATAACAGGTAAAAAATGACAAAACCG
1 GTGTCGATACTTTATAAAAATATATCGATCTATAACAATATAACAGGTAAAAAATGACAAAACCG
4410172 GTCTATAAATGACAAAACAGGTAAAGCGCTATCGAATATATTGAAA
66 GTCTATAAATGACAAAACAGGTAAAGCGCTATCGAATATATTGAAA
* * * * * *
4410218 GTTTCGATACTTTATAGAAATGTATTGATCTATAACAATATAACAGGTAAAAAATGATAAAATCG
1 GTGTCGATACTTTATAAAAATATATCGATCTATAACAATATAACAGGTAAAAAATGACAAAACCG
* *
4410283 GTCTATAAATGACAAAACAGGTAAAGCGCTATCGGATATATTGAGA
66 GTCTATAAATGACAAAACAGGTAAAGCGCTATCGAATATATTGAAA
* *
4410329 GTGTCGATATTTTATAAAAATATATCGATCAATAACAATATAACAGGTAAACAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCTATAACAATATAACAGGTAAA-AAATGACAAAACC
* * * * *
4410394 GGTCAATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATA
65 GGTCTATAAATGACAAAACAGGTAAAGCGCTATCGAATATATTGAAA
4410441 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
4410456 TATAAGTATC
Statistics
Matches: 322, Mismatches: 25, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
111 211 0.66
112 110 0.34
113 1 0.00
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (111 bp):
GTGTCGATACTTTATAAAAATATATCGATCTATAACAATATAACAGGTAAAAAATGACAAAACCG
GTCTATAAATGACAAAACAGGTAAAGCGCTATCGAATATATTGAAA
Found at i:4410409 original size:223 final size:223
Alignment explanation
Indices: 4409995--4410455 Score: 746
Period size: 223 Copynumber: 2.1 Consensus size: 223
4409985 TTGTCGGTTT
*
4409995 GTGTCGATACTTTATAAAAAAATATTATTCTATAATAATATAACAGGTAAAAAAATGACAAAATC
1 GTGTCGATACTTTATAAAAAAATATTATTCTATAACAATATAACAGGTAAAAAAATGACAAAATC
4410060 GGTCTATAAATGACAAAACAGGTAAAGCGCTATCGAATATATTGAAAGTGTCGATACTTTATAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTATCGAATATATTGAAAGTGTCGATACTTTATAAA
* * *
4410125 AATGTATCGATCTATAACAATATAACAGGTAAAAAATGACAAAACCGGTCTATAAATGACAAAAC
131 AATATATCGATCAATAACAATATAACAGGTAAAAAATGACAAAACCGGTCAATAAATGACAAAAC
*
4410190 AGGTAAAGCGCTATCGAATATATTGAAA
196 AGGTAAAGCGCTACCGAATATATTGAAA
* * ** *
4410218 GTTTCGATACTTTATAGAAATGTATTGA-TCTATAACAATATAACAGGT-AAAAAATGATAAAAT
1 GTGTCGATACTTTATAAAAAAATATT-ATTCTATAACAATATAACAGGTAAAAAAATGACAAAAT
* * *
4410281 CGGTCTATAAATGACAAAACAGGTAAAGCGCTATCGGATATATTGAGAGTGTCGATATTTTATAA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTATCGAATATATTGAAAGTGTCGATACTTTATAA
4410346 AAATATATCGATCAATAACAATATAACAGGTAAACAAATGACAAAACCGGTCAATAAATGACAAA
130 AAATATATCGATCAATAACAATATAACAGGTAAA-AAATGACAAAACCGGTCAATAAATGACAAA
* * *
4410411 ACAGGTAAAGCGCTACCGGATATGTTGATA
194 ACAGGTAAAGCGCTACCGAATATATTGAAA
4410441 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
4410456 TATAAGTATC
Statistics
Matches: 219, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
222 108 0.49
223 110 0.50
224 1 0.00
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (223 bp):
GTGTCGATACTTTATAAAAAAATATTATTCTATAACAATATAACAGGTAAAAAAATGACAAAATC
GGTCTATAAATGACAAAACAGGTAAAGCGCTATCGAATATATTGAAAGTGTCGATACTTTATAAA
AATATATCGATCAATAACAATATAACAGGTAAAAAATGACAAAACCGGTCAATAAATGACAAAAC
AGGTAAAGCGCTACCGAATATATTGAAA
Found at i:4410651 original size:294 final size:294
Alignment explanation
Indices: 4410215--4410887 Score: 999
Period size: 294 Copynumber: 2.3 Consensus size: 294
4410205 GAATATATTG
* * * * *
4410215 AAAGTTTCGATACTTTATAGAAATGTATTGATCTATAACAATATAACAGGTAAAAA-ATGATAAA
1 AAAGTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACATGTAAAAATATGACAAA
** * * * * * *
4410279 ATCGGTCTATAAATGACAAAACAGGTAAAGCGCTATCGGATATATTGAGAGTGTCGATATTTTAT
66 ATCGGTCTCGAAATGACAAAACAGATAAAGAGCTACCGGATATATTGAAAGTGTCAATACTTTAT
* *
4410344 AAAAATATATCGATCAATAACAATATAACAGGTAAACAA-ATGACAAAACCGGTCAATAAATGAC
131 AAAAATATATCGATCAATAACAATATAACAGGTAAA-AATATGACAAAACCGATCAAGAAATGAC
* * *
4410408 AAAACAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTATTATAAGTATCTACACTT
195 AAAACAGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTATTATAAGTATCGACACTT
* * * *
4410473 TTGGAATTTAAAAGAGAAGAAGTTATATCGTTAAT
260 TTGAAATTTAAAAGAAAAGAAGTTATAGCGTCAAT
4410508 AAAGTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACATGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACATGTAAAAATATGACAAA
* * *
4410573 ACCGGTCTCGAAATGACAAAACCGATAAAGAGCTACCGGATATGTTGAAAGTGTCAATACTTTAT
66 ATCGGTCTCGAAATGACAAAACAGATAAAGAGCTACCGGATATATTGAAAGTGTCAATACTTTAT
* * * **
4410638 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATCGATCTCGAAATGACA
131 AAAAATATATCGATCAATAACAATATAACAGGTAAAAATATGACAAAACCGATCAAGAAATGACA
* * *
4410703 AAACCGGTAAAGAGCTACTGGATATTTTGAAAGTGTCGATACTTTATTATAAGTATCGACACTTT
196 AAACAGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTATTATAAGTATCGACACTTT
*
4410768 TGAAATTTAAAATAAAAGAAGTTATAGCGTCAAT
261 TGAAATTTAAAAGAAAAGAAGTTATAGCGTCAAT
* *
4410802 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATGTGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACATGTAAAAATATGACAAA
4410867 ATCGGTCTCGAAATGACAAAA
66 ATCGGTCTCGAAATGACAAAA
4410888 TCAATAGTAA
Statistics
Matches: 341, Mismatches: 37, Indels: 3
0.90 0.10 0.01
Matches are distributed among these distances:
293 54 0.16
294 287 0.84
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.28
Consensus pattern (294 bp):
AAAGTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACATGTAAAAATATGACAAA
ATCGGTCTCGAAATGACAAAACAGATAAAGAGCTACCGGATATATTGAAAGTGTCAATACTTTAT
AAAAATATATCGATCAATAACAATATAACAGGTAAAAATATGACAAAACCGATCAAGAAATGACA
AAACAGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTATTATAAGTATCGACACTTT
TGAAATTTAAAAGAAAAGAAGTTATAGCGTCAAT
Found at i:4410705 original size:112 final size:112
Alignment explanation
Indices: 4410508--4410749 Score: 412
Period size: 112 Copynumber: 2.2 Consensus size: 112
4410498 TATCGTTAAT
* *
4410508 AAAGTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACATGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
*
4410573 ACCGGTCTCGAAATGACAAAACCGATAAAGAGCTACCGGATATGTTG
66 ACCGATCTCGAAATGACAAAACCGATAAAGAGCTACCGGATATGTTG
*
4410620 AAAGTGTCAATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* * * *
4410685 ATCGATCTCGAAATGACAAAACCGGTAAAGAGCTACTGGATATTTTG
66 ACCGATCTCGAAATGACAAAACCGATAAAGAGCTACCGGATATGTTG
4410732 AAAGTGTCGATACTTTAT
1 AAAGTGTCGATACTTTAT
4410750 TATAAGTATC
Statistics
Matches: 121, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
112 121 1.00
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.26
Consensus pattern (112 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
ACCGATCTCGAAATGACAAAACCGATAAAGAGCTACCGGATATGTTG
Found at i:4411564 original size:22 final size:22
Alignment explanation
Indices: 4411529--4411572 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
4411519 AAATAGGTCA
*
4411529 ATATAAGCATTACC-AATTATAT
1 ATATAAGCACTACCTAA-TATAT
*
4411551 ATATAAGCGCTACCTAATATAT
1 ATATAAGCACTACCTAATATAT
4411573 TATTGTACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (22 bp):
ATATAAGCACTACCTAATATAT
Found at i:4415948 original size:116 final size:118
Alignment explanation
Indices: 4415677--4415955 Score: 429
Period size: 118 Copynumber: 2.4 Consensus size: 118
4415667 ATCTCTACTA
* * * * *
4415677 CACACCAGTAAGGACTTACCATGAGTACATAGTAAAGGAGTCTGCGGTAATAACTACCCCTATCC
1 CACACCAGTAAGGACTTACCATGAGCACACAGCAAAAGAGCCTGCGGTAATAACTACCCCTATCC
* *
4415742 AATCACTCCGATCACCAGATTGTGTAGGTTTCCCATAACCATACACCCACCTG
66 AATCACTCCGATCACCAGATTATGTAGGTTTCCCATAACCATACACCCACATG
* *
4415795 CACACCAGTAAGGACTTACCCTGAGCACACAACAAAAGAGCCTGCGGTAATAACTA-CCCTAATC
1 CACACCAGTAAGGACTTACCATGAGCACACAGCAAAAGAGCCTGCGGTAATAACTACCCCT-ATC
4415859 CAATCACTCCGATCA-CAGATTATGTAGGTTTCCCATAACCATACA-CCACATG
65 CAATCACTCCGATCACCAGATTATGTAGGTTTCCCATAACCATACACCCACATG
* *
4415911 CACACCATTAAGGACTTACCTTGAGCACACAGCAAAAGAGCCTGC
1 CACACCAGTAAGGACTTACCATGAGCACACAGCAAAAGAGCCTGC
4415956 AATACTTCAT
Statistics
Matches: 148, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
116 48 0.32
117 33 0.22
118 67 0.45
ACGTcount: A:0.34, C:0.30, G:0.15, T:0.20
Consensus pattern (118 bp):
CACACCAGTAAGGACTTACCATGAGCACACAGCAAAAGAGCCTGCGGTAATAACTACCCCTATCC
AATCACTCCGATCACCAGATTATGTAGGTTTCCCATAACCATACACCCACATG
Found at i:4422304 original size:21 final size:21
Alignment explanation
Indices: 4422279--4422324 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
4422269 ACTTTATGTG
*
4422279 TCAAGATAACATTGTGTGTAT
1 TCAAGATAACATTATGTGTAT
*
4422300 TCAAGATAGCATTATGTGTAT
1 TCAAGATAACATTATGTGTAT
4422321 TCAA
1 TCAA
4422325 ACTCTGCTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (21 bp):
TCAAGATAACATTATGTGTAT
Found at i:4422505 original size:16 final size:17
Alignment explanation
Indices: 4422475--4422517 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
4422465 ATGTTTTGAC
4422475 TTAA-TATTTTGATAAT
1 TTAATTATTTTGATAAT
4422491 TTAATTATTTT-ATAAT
1 TTAATTATTTTGATAAT
*
4422507 TGTAATAATTT
1 T-TAATTATTT
4422518 CCAATTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 10 0.42
17 14 0.58
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (17 bp):
TTAATTATTTTGATAAT
Found at i:4423655 original size:15 final size:14
Alignment explanation
Indices: 4423634--4423690 Score: 60
Period size: 14 Copynumber: 4.0 Consensus size: 14
4423624 ATTGATTTTC
*
4423634 TGGAAATTGAATTA
1 TGGAAAATGAATTA
*
4423648 TGGAAAATAAATTA
1 TGGAAAATGAATTA
** *
4423662 CTGGAATTTGAATTC
1 -TGGAAAATGAATTA
4423677 TGGAAAATGAATTA
1 TGGAAAATGAATTA
4423691 CATTTCTGGA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
14 23 0.70
15 10 0.30
ACGTcount: A:0.44, C:0.04, G:0.19, T:0.33
Consensus pattern (14 bp):
TGGAAAATGAATTA
Found at i:4423675 original size:29 final size:29
Alignment explanation
Indices: 4423633--4423691 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
4423623 AATTGATTTT
4423633 CTGGAAATTGAATTATGGAAAATAAATTA
1 CTGGAAATTGAATTATGGAAAATAAATTA
* * *
4423662 CTGGAATTTGAATTCTGGAAAATGAATTA
1 CTGGAAATTGAATTATGGAAAATAAATTA
4423691 C
1 C
4423692 ATTTCTGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.32
Consensus pattern (29 bp):
CTGGAAATTGAATTATGGAAAATAAATTA
Found at i:4423732 original size:14 final size:14
Alignment explanation
Indices: 4423693--4423732 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
4423683 ATGAATTACA
* *
4423693 TTTCTGGAAAACGT
1 TTTCCGGAAAATGT
4423707 TTTCCGGAAAATGT
1 TTTCCGGAAAATGT
*
4423721 TTTCCGTAAAAT
1 TTTCCGGAAAAT
4423733 AAATTACATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (14 bp):
TTTCCGGAAAATGT
Found at i:4424108 original size:28 final size:29
Alignment explanation
Indices: 4424072--4424127 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
4424062 TAAATATCTT
* *
4424072 TATTAAAATAT-TATTAGATTATTTATTAA
1 TATTAAAATATATAATA-ATTATTCATTAA
4424101 TATT-AAATATATAATAATTATTCATTA
1 TATTAAAATATATAATAATTATTCATTA
4424128 TTAAAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (29 bp):
TATTAAAATATATAATAATTATTCATTAA
Found at i:4424237 original size:27 final size:25
Alignment explanation
Indices: 4424178--4424238 Score: 61
Period size: 27 Copynumber: 2.4 Consensus size: 25
4424168 ATATAAATTT
4424178 TATTAATAATTTATATATTATAAAA
1 TATTAATAATTTATATATTATAAAA
** *
4424203 TAAAAATATATATTATATTATTA-GAAA
1 TATTAATA-AT-TTATA-TATTATAAAA
4424230 TATTAATAA
1 TATTAATAA
4424239 ATACATTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
25 6 0.21
26 3 0.11
27 14 0.50
28 5 0.18
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
TATTAATAATTTATATATTATAAAA
Found at i:4428119 original size:37 final size:36
Alignment explanation
Indices: 4428049--4428119 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 36
4428039 ATTTTTAATT
*
4428049 TTTTTTAAAAAAATTATATAAATATTATGAATTTAA
1 TTTTTTAAAAAAATTATATAAATATTATCAATTTAA
*
4428085 TTTTTTAAAGAAAA-TATATAAATATTTTACAATTT
1 TTTTTTAAA-AAAATTATATAAATATTAT-CAATTT
4428120 GTAATATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 22 0.71
37 9 0.29
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (36 bp):
TTTTTTAAAAAAATTATATAAATATTATCAATTTAA
Found at i:4431750 original size:25 final size:25
Alignment explanation
Indices: 4431722--4431792 Score: 92
Period size: 25 Copynumber: 2.9 Consensus size: 25
4431712 AGAAAAAAAT
*
4431722 TATTTTTTAAATAATAATTTGAATA
1 TATTTTTTAAATAATAAATTGAATA
*
4431747 TATTTTTTAAATAATAAATTGAA-G
1 TATTTTTTAAATAATAAATTGAATA
* *
4431771 T-TTTTTAAAATAAAAAATTGAA
1 TATTTTTTAAATAATAAATTGAA
4431793 ATTTTATATG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 19 0.45
24 1 0.02
25 22 0.52
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (25 bp):
TATTTTTTAAATAATAAATTGAATA
Found at i:4431781 original size:23 final size:22
Alignment explanation
Indices: 4431723--4431797 Score: 87
Period size: 23 Copynumber: 3.2 Consensus size: 22
4431713 GAAAAAAATT
*
4431723 ATTTTTTAAATAATAATTTGAATA
1 ATTTTTTAAATAATAAATTG-A-A
4431747 TATTTTTTAAATAATAAATTGAA
1 -ATTTTTTAAATAATAAATTGAA
* *
4431770 GTTTTTTAAAATAAAAAATTGAA
1 ATTTTTT-AAATAATAAATTGAA
4431793 ATTTT
1 ATTTT
4431798 ATATGTCTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
22 6 0.13
23 19 0.42
24 1 0.02
25 19 0.42
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (22 bp):
ATTTTTTAAATAATAAATTGAA
Found at i:4431948 original size:18 final size:18
Alignment explanation
Indices: 4431925--4431959 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
4431915 TTTTAGATCA
4431925 TTTAAACACCTAAAATTC
1 TTTAAACACCTAAAATTC
4431943 TTTAAACACCTAAAATT
1 TTTAAACACCTAAAATT
4431960 AAGTTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (18 bp):
TTTAAACACCTAAAATTC
Found at i:4435386 original size:23 final size:22
Alignment explanation
Indices: 4435359--4435402 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
4435349 TATATATATA
*
4435359 TATATAATTAGTTATTTATATGT
1 TATATAATTA-TTAATTATATGT
*
4435382 TATATTATTATTAATTATATG
1 TATATAATTATTAATTATATG
4435403 GGTTAACTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (22 bp):
TATATAATTATTAATTATATGT
Found at i:4435634 original size:16 final size:15
Alignment explanation
Indices: 4435613--4435649 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
4435603 TGAGTATATT
4435613 TATAAATAATATTATA
1 TATAAATAATATT-TA
4435629 TATAAATAATATTTA
1 TATAAATAATATTTA
4435644 T-TAAAT
1 TATAAAT
4435650 GTTCTTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 5 0.24
15 3 0.14
16 13 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TATAAATAATATTTA
Found at i:4436414 original size:24 final size:24
Alignment explanation
Indices: 4436387--4436443 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
4436377 GAACGTTGGA
*
4436387 TTATATTCGTTCATTTATGTTTAT
1 TTATATTCGTTCATTTATGTTAAT
4436411 TTATATTCGTTCATTTATGTTAAT
1 TTATATTCGTTCATTTATGTTAAT
*
4436435 TTATGTTCG
1 TTATATTCG
4436444 AACAGATGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.21, C:0.09, G:0.11, T:0.60
Consensus pattern (24 bp):
TTATATTCGTTCATTTATGTTAAT
Found at i:4436744 original size:20 final size:20
Alignment explanation
Indices: 4436711--4436750 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
4436701 TCGTTTATTT
* *
4436711 CGTTCGTTTGTGTTCGTTTA
1 CGTTCATTTATGTTCGTTTA
*
4436731 CGTTCATTTATGTTTGTTTA
1 CGTTCATTTATGTTCGTTTA
4436751 TCATTTAATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.10, C:0.12, G:0.20, T:0.57
Consensus pattern (20 bp):
CGTTCATTTATGTTCGTTTA
Found at i:4438840 original size:365 final size:365
Alignment explanation
Indices: 4438171--4438902 Score: 1394
Period size: 365 Copynumber: 2.0 Consensus size: 365
4438161 GTTTCTGGAA
4438171 CACCATGTGGAGCTGTAGCTGCAGAAGCTAAGCAAGCTCAAGCTAGTTGGGTTGTATTGGACAAG
1 CACCATGTGGAGCTGTAGCTGCAGAAGCTAAGCAAGCTCAAGCTAGTTGGGTTGTATTGGACAAG
4438236 TAACATCGTGTTTGCAGTGTTTCTTCTTCCTTTCTTTTCATTTGTGTTCTATCCAAAAAGGTATA
66 TAACATCGTGTTTGCAGTGTTTCTTCTTCCTTTCTTTTCATTTGTGTTCTATCCAAAAAGGTATA
4438301 TGCACATGCTTGCAGTATCCTCATTTTCTTTAATTTTTTTCAGGCAGCTCAAACACGAGGAAAAG
131 TGCACATGCTTGCAGTATCCTCATTTTCTTTAATTTTTTTCAGGCAGCTCAAACACGAGGAAAAG
* *
4438366 CGCTGCATGGAGGAGTTGCAATATAACATAGTGATTATGAAGCGTTCTCAGGCAAAAGTGCTGCG
196 CGCTGAATGGAGGAGTTGCAATACAACATAGTGATTATGAAGCGTTCTCAGGCAAAAGTGCTGCG
4438431 CTTAAATTTGGTTGGGGCATCTGAGAAGGAAGCTGAAGCTTGTCAATTAAATCCCGAGACAGATG
261 CTTAAATTTGGTTGGGGCATCTGAGAAGGAAGCTGAAGCTTGTCAATTAAATCCCGAGACAGATG
4438496 AAATATCTGAAAAGCATCCTAAAAAC-AAAAATGCATCAT
326 AAATATCTGAAAAGCATCCTAAAAACAAAAAATGCATCAT
4438535 CACCATGTGGAGCTGTAGCTGCAGAAGCTAAGCAAGCTCAAGCTAGTTGGGTTGTATTGGACAAG
1 CACCATGTGGAGCTGTAGCTGCAGAAGCTAAGCAAGCTCAAGCTAGTTGGGTTGTATTGGACAAG
* *
4438600 TAACATCGTGTTTGCATTGTTTCTTCTTCCTTTCTTTTCCTTTTGTGTTCTATCCAAAAAGGTAT
66 TAACATCGTGTTTGCAGTGTTTCTTCTTCCTTTCTTTT-CATTTGTGTTCTATCCAAAAAGGTAT
4438665 ATGCACATGCTTGCAGTATCCTCATTTTCTTTAATTTTTTTCAGGCAGCTCAAACACGAGGAAAA
130 ATGCACATGCTTGCAGTATCCTCATTTTCTTTAATTTTTTTCAGGCAGCTCAAACACGAGGAAAA
*
4438730 GCGCTGAATGGAGGAGTTGCAATGCAACATAGTGATTATGAAGCGTTCTCAGGCAAAAGTGCTGC
195 GCGCTGAATGGAGGAGTTGCAATACAACATAGTGATTATGAAGCGTTCTCAGGCAAAAGTGCTGC
4438795 GCTTAAATTTGGTTGGGGCATCTGAGAAGGAAGCTGAAGCTTGTCAATTAAATCCCGAGACAGAT
260 GCTTAAATTTGGTTGGGGCATCTGAGAAGGAAGCTGAAGCTTGTCAATTAAATCCCGAGACAGAT
4438860 GAAATATCTGAAAAGCATCCTAAAAACAAAAAAATGCATCAT
325 GAAATATCTGAAAAGCATCCTAAAAAC-AAAAAATGCATCAT
4438902 C
1 C
4438903 CGAATCTATT
Statistics
Matches: 360, Mismatches: 5, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
364 102 0.28
365 244 0.68
367 14 0.04
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (365 bp):
CACCATGTGGAGCTGTAGCTGCAGAAGCTAAGCAAGCTCAAGCTAGTTGGGTTGTATTGGACAAG
TAACATCGTGTTTGCAGTGTTTCTTCTTCCTTTCTTTTCATTTGTGTTCTATCCAAAAAGGTATA
TGCACATGCTTGCAGTATCCTCATTTTCTTTAATTTTTTTCAGGCAGCTCAAACACGAGGAAAAG
CGCTGAATGGAGGAGTTGCAATACAACATAGTGATTATGAAGCGTTCTCAGGCAAAAGTGCTGCG
CTTAAATTTGGTTGGGGCATCTGAGAAGGAAGCTGAAGCTTGTCAATTAAATCCCGAGACAGATG
AAATATCTGAAAAGCATCCTAAAAACAAAAAATGCATCAT
Found at i:4445894 original size:43 final size:43
Alignment explanation
Indices: 4445844--4446071 Score: 181
Period size: 42 Copynumber: 5.3 Consensus size: 43
4445834 ATTAGGCTTT
4445844 TAAGTTTTTTCAATCTCACTTTCTACATTTCAATTGAGGCCTC
1 TAAGTTTTTTCAATCTCACTTTCTACATTTCAATTGAGGCCTC
* *
4445887 TAAG-TTTTTCAATCTCAATTTCTACATTAT-AATTGAGGCCCC
1 TAAGTTTTTTCAATCTCACTTTCTACATT-TCAATTGAGGCCTC
* * * *
4445929 TAA-TTTTTTTAAACTCACTTTTTTA-ACTTTATAATTGAGGCC-C
1 TAAGTTTTTTCAATCTCAC-TTTCTACA-TTT-CAATTGAGGCCTC
*
4445972 TTAAGTTTTTT-AATCTCACTTTCTA-ACTTACTAATTGAGG-CTCC
1 -TAAGTTTTTTCAATCTCACTTTCTACA-TTTC-AATTGAGGCCT-C
* * * * *
4446016 T--GTTTTTTTAATCTCAATTTCTACCTTTATAATTAAGGCCTC
1 TAAGTTTTTTCAATCTCACTTTCTACATTT-CAATTGAGGCCTC
4446058 TAA-TTTTTTACAAT
1 TAAGTTTTTT-CAAT
4446072 TTCATAAAAT
Statistics
Matches: 151, Mismatches: 16, Indels: 35
0.75 0.08 0.17
Matches are distributed among these distances:
41 7 0.05
42 75 0.50
43 39 0.26
44 24 0.16
45 6 0.04
ACGTcount: A:0.26, C:0.19, G:0.08, T:0.46
Consensus pattern (43 bp):
TAAGTTTTTTCAATCTCACTTTCTACATTTCAATTGAGGCCTC
Found at i:4445977 original size:86 final size:86
Alignment explanation
Indices: 4445875--4446071 Score: 233
Period size: 86 Copynumber: 2.3 Consensus size: 86
4445865 TCTACATTTC
4445875 AATTGAGG-CCTCTAAGTTTTTCAATCTCAATTTCT-ACATTA-TAATTGAGGCCCCTAATTTTT
1 AATTGAGGCCCTCTAAGTTTTTCAATCTCAATTTCTAAC-TTACTAATTGAGGCCCCT-ATTTTT
* *
4445937 TTAAACTCACTTTTTTAACTTTAT
64 TTAAACTCA-ATTTCTAACTTTAT
* * * *
4445961 AATTGAGGCCCT-TAAGTTTTTTAATCTCACTTTCTAACTTACTAATTGAGGCTCCTGTTTTTTT
1 AATTGAGGCCCTCTAAGTTTTTCAATCTCAATTTCTAACTTACTAATTGAGGCCCCTATTTTTTT
* *
4446025 AATCTCAATTTCTACCTTTAT
66 AAACTCAATTTCTAACTTTAT
* *
4446046 AATTAAGG-CCTCTAATTTTTTACAAT
1 AATTGAGGCCCTCTAAGTTTTT-CAAT
4446072 TTCATAAAAT
Statistics
Matches: 95, Mismatches: 11, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
84 3 0.03
85 26 0.27
86 48 0.51
87 18 0.19
ACGTcount: A:0.27, C:0.19, G:0.09, T:0.46
Consensus pattern (86 bp):
AATTGAGGCCCTCTAAGTTTTTCAATCTCAATTTCTAACTTACTAATTGAGGCCCCTATTTTTTT
AAACTCAATTTCTAACTTTAT
Found at i:4446067 original size:128 final size:122
Alignment explanation
Indices: 4445785--4446067 Score: 324
Period size: 128 Copynumber: 2.2 Consensus size: 122
4445775 ATCCCTTTTT
* ** **
4445785 TACCTTTATAATTGAGGCACCTAATTTTGTAGCCTCACTTTTAACTTTAATTAGGCTTTTAAGTT
1 TACCTTTATAATTGAGGC-CCTAATTTTTTAAACTCACTTTTAACTTTAATTAGGCCCTTAAGTT
*
4445850 TTTTCAATCTCACTTTCTACATTTCAATTGAGGCCTCTAAGTTTTTCAATCTCAATTTC
65 TTTTCAATCTCACTTTCTACATTACAATTGAGGCCTCT-AGTTTTTCAATCTCAATTTC
*
4445909 TA-CATTATAATTGAGGCCCCTAATTTTTTTAAACTCACTTTTTTAACTTTATAATTGAGGCCCT
1 TACCTTTATAATTGAGG-CCCTAA-TTTTTTAAACTCAC--TTTTAAC-TT-TAATT-AGGCCCT
*
4445973 TAAGTTTTTT-AATCTCACTTTCTA-ACTTACTAATTGAGG-CTCCT-GTTTTTTTAATCTCAAT
59 TAAGTTTTTTCAATCTCACTTTCTACA-TTAC-AATTGAGGCCT-CTAG-TTTTTCAATCTCAAT
4446034 TTC
120 TTC
*
4446037 TACCTTTATAATTAAGGCCTCTAATTTTTTA
1 TACCTTTATAATTGAGGCC-CTAATTTTTTA
4446068 CAATTTCATA
Statistics
Matches: 136, Mismatches: 10, Indels: 22
0.81 0.06 0.13
Matches are distributed among these distances:
123 18 0.13
124 14 0.10
126 7 0.05
127 4 0.03
128 52 0.38
129 41 0.30
ACGTcount: A:0.26, C:0.19, G:0.09, T:0.46
Consensus pattern (122 bp):
TACCTTTATAATTGAGGCCCTAATTTTTTAAACTCACTTTTAACTTTAATTAGGCCCTTAAGTTT
TTTCAATCTCACTTTCTACATTACAATTGAGGCCTCTAGTTTTTCAATCTCAATTTC
Found at i:4468578 original size:15 final size:15
Alignment explanation
Indices: 4468558--4468605 Score: 78
Period size: 15 Copynumber: 3.2 Consensus size: 15
4468548 TTAGCTGGGT
*
4468558 GGGCGGATGTGGGGC
1 GGGCGGATGCGGGGC
*
4468573 GGGCGGATGCGGGAC
1 GGGCGGATGCGGGGC
4468588 GGGCGGATGCGGGGC
1 GGGCGGATGCGGGGC
4468603 GGG
1 GGG
4468606 TAATGTCTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.08, C:0.17, G:0.67, T:0.08
Consensus pattern (15 bp):
GGGCGGATGCGGGGC
Found at i:4475834 original size:12 final size:12
Alignment explanation
Indices: 4475817--4475842 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4475807 TTCCTGCTTA
4475817 CTTGTATTAGTT
1 CTTGTATTAGTT
4475829 CTTGTATTAGTT
1 CTTGTATTAGTT
4475841 CT
1 CT
4475843 GGTGTCCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.58
Consensus pattern (12 bp):
CTTGTATTAGTT
Found at i:4478759 original size:18 final size:18
Alignment explanation
Indices: 4478742--4478774 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4478732 CAATTTAATT
4478742 TTTC-GATG-AAATTCAA
1 TTTCTGATGTAAATTCAA
4478758 TTTCTGATGTAAATTCA
1 TTTCTGATGTAAATTCA
4478775 TTTATTATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 4 0.27
18 7 0.47
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (18 bp):
TTTCTGATGTAAATTCAA
Found at i:4481403 original size:75 final size:77
Alignment explanation
Indices: 4481294--4481503 Score: 284
Period size: 75 Copynumber: 2.8 Consensus size: 77
4481284 CCGTTGTACA
* * *
4481294 AGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
**
4481358 -CAAAACTGTTT
66 CCAAAACCATTT
* * * *
4481369 A-GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCATCCGAGCATTCTGGAAATCTCGGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
4481433 CCAAAACCATTT
66 CCAAAACCATTT
*
4481445 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCA-ATCTGGAATT
1 AGGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATA-CTGGAATT
4481504 TTTGGCTTTG
Statistics
Matches: 117, Mismatches: 13, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
74 17 0.15
75 39 0.33
76 10 0.09
77 21 0.18
78 30 0.26
ACGTcount: A:0.20, C:0.23, G:0.33, T:0.24
Consensus pattern (77 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
CCAAAACCATTT
Found at i:4482115 original size:15 final size:15
Alignment explanation
Indices: 4482097--4482138 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
4482087 AACATCCATA
*
4482097 AATCCAAAATCCAAC
1 AATCCAAAATCAAAC
4482112 AATCCACAAAATCAAAC
1 AAT-C-CAAAATCAAAC
4482129 AATCCAAAAT
1 AATCCAAAAT
4482139 ATAATGTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 9 0.38
16 2 0.08
17 13 0.54
ACGTcount: A:0.57, C:0.29, G:0.00, T:0.14
Consensus pattern (15 bp):
AATCCAAAATCAAAC
Done.