Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007957.1 Hibiscus syriacus cultivar Beakdansim tig00110384_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: 8646418
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 30 of 43
Found at i:6006897 original size:20 final size:19
Alignment explanation
Indices: 6006874--6006918 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
6006864 ATTTTTCATT
*
6006874 AAAACAATATAATTAAATCA
1 AAAACAACA-AATTAAATCA
* *
6006894 AAAACAACAATTTGAATCA
1 AAAACAACAAATTAAATCA
6006913 AAAACA
1 AAAACA
6006919 TTTTTTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.64, C:0.13, G:0.02, T:0.20
Consensus pattern (19 bp):
AAAACAACAAATTAAATCA
Found at i:6010335 original size:18 final size:18
Alignment explanation
Indices: 6010314--6010348 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6010304 ATCTTTATTT
*
6010314 ATTTAATCTCTTTTTACC
1 ATTTAATCTCATTTTACC
*
6010332 ATTTAATTTCATTTTAC
1 ATTTAATCTCATTTTAC
6010349 TAAAACCCCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.17, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTAATCTCATTTTACC
Found at i:6013356 original size:41 final size:41
Alignment explanation
Indices: 6013299--6013378 Score: 160
Period size: 41 Copynumber: 2.0 Consensus size: 41
6013289 CCCACTACAC
6013299 TCCAATCAGACCTTCCTTTTTGGTTCAATCCATGGAAACAG
1 TCCAATCAGACCTTCCTTTTTGGTTCAATCCATGGAAACAG
6013340 TCCAATCAGACCTTCCTTTTTGGTTCAATCCATGGAAAC
1 TCCAATCAGACCTTCCTTTTTGGTTCAATCCATGGAAAC
6013379 GTAATATTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.33
Consensus pattern (41 bp):
TCCAATCAGACCTTCCTTTTTGGTTCAATCCATGGAAACAG
Found at i:6022660 original size:231 final size:230
Alignment explanation
Indices: 6022258--6022684 Score: 755
Period size: 231 Copynumber: 1.9 Consensus size: 230
6022248 GACAGGACCC
* * *
6022258 GACCCGAACCGAAAATATATATAATTTTACCTTATATATTTAGAAATAATTATAATAATACCTCT
1 GACCCGAACCGAAAAAATATATAATTTTACCTTATATATTTAGAAATAATTACAATAATACCCCT
*
6022323 CTATATATAATATTTTTAATTAAATCACTGTTTTTATTGAATAAAAATAATTTTTTTATTATTTC
66 CTATATATAATATTTTTAATTAAATCACTATTTTTATTGAATAAAAATAATTTTTTTATTATTTC
*
6022388 GGGTCGGGTCGAGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGG
131 GGGTCGGGTCGAGTTTCTAATTCATATATTCAGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGG
6022453 TTGGGTTGGGTTCGGGTTTAGGGTGAAAAATACCT
196 TTGGGTTGGGTTCGGGTTTAGGGTGAAAAATACCT
* *
6022488 GACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCT
1 GACCCGAACCGAAAAAATATATAATTTTACCTTATATATTTAGAAATAATTACAATAATACCCCT
* *
6022553 CTATATATAATTTTTTTCAATTAAGTCACTATTTTTATTGAATAAAAATAATTTTTTTATTATTT
66 CTATATATAATATTTTT-AATTAAATCACTATTTTTATTGAATAAAAATAATTTTTTTATTATTT
*
6022618 CGGGTCGGGTCGGGTTTCTAATTCATATATTCAGGTCGGGTCGGGTGAAACTTTATTTTGGTCGG
130 CGGGTCGGGTCGAGTTTCTAATTCATATATTCAGGTCGGGTCGGGTGAAACTTTATTTTGGTCGG
6022683 GT
195 GT
6022685 CGGTCTCGGA
Statistics
Matches: 186, Mismatches: 10, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
230 76 0.41
231 110 0.59
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (230 bp):
GACCCGAACCGAAAAAATATATAATTTTACCTTATATATTTAGAAATAATTACAATAATACCCCT
CTATATATAATATTTTTAATTAAATCACTATTTTTATTGAATAAAAATAATTTTTTTATTATTTC
GGGTCGGGTCGAGTTTCTAATTCATATATTCAGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGG
TTGGGTTGGGTTCGGGTTTAGGGTGAAAAATACCT
Found at i:6023020 original size:17 final size:18
Alignment explanation
Indices: 6022994--6023039 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
6022984 TATGGAATTG
*
6022994 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
*
6023011 GATTCTAATTCCTTCACA
1 GATTCCAATTCCTTCACA
6023029 GATTCCAATTC
1 GATTCCAATTC
6023040 TCTCCGAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.35
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:6034476 original size:19 final size:19
Alignment explanation
Indices: 6034454--6034497 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
6034444 CTAAACGGCT
6034454 TGGCTCGCCTCGATCCAAA
1 TGGCTCGCCTCGATCCAAA
*
6034473 TGGCTCGGCTCGATCCAAA
1 TGGCTCGCCTCGATCCAAA
6034492 TGGCTC
1 TGGCTC
6034498 AGATTGGTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.18, C:0.34, G:0.25, T:0.23
Consensus pattern (19 bp):
TGGCTCGCCTCGATCCAAA
Found at i:6034477 original size:24 final size:24
Alignment explanation
Indices: 6034438--6034484 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
6034428 CTCGACTCAG
* *
6034438 CTCGATCTAAACGGCTTGGCTCGC
1 CTCGATCCAAACGGCTCGGCTCGC
*
6034462 CTCGATCCAAATGGCTCGGCTCG
1 CTCGATCCAAACGGCTCGGCTCG
6034485 ATCCAAATGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.17, C:0.34, G:0.26, T:0.23
Consensus pattern (24 bp):
CTCGATCCAAACGGCTCGGCTCGC
Found at i:6034508 original size:19 final size:19
Alignment explanation
Indices: 6034463--6034501 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
6034453 TTGGCTCGCC
* *
6034463 TCGATCCAAATGGCTCGGC
1 TCGATCCAAATGGCTCAGA
6034482 TCGATCCAAATGGCTCAGA
1 TCGATCCAAATGGCTCAGA
6034501 T
1 T
6034502 TGGTCCAGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (19 bp):
TCGATCCAAATGGCTCAGA
Found at i:6038313 original size:17 final size:17
Alignment explanation
Indices: 6038291--6038325 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
6038281 CTGGCCTGAC
*
6038291 CCGACCCGACCCGTTGA
1 CCGACCCGACCCGGTGA
6038308 CCGACCCGACCCGGTGA
1 CCGACCCGACCCGGTGA
6038325 C
1 C
6038326 ATTATGGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.17, C:0.49, G:0.26, T:0.09
Consensus pattern (17 bp):
CCGACCCGACCCGGTGA
Found at i:6038362 original size:29 final size:29
Alignment explanation
Indices: 6038320--6038430 Score: 163
Period size: 29 Copynumber: 3.9 Consensus size: 29
6038310 GACCCGACCC
6038320 GGTGACATTATGGGAAATATTTTGAAAAA
1 GGTGACATTATGGGAAATATTTTGAAAAA
* *
6038349 GGTGACATTTTGGGAATTATTTTGAAAAA
1 GGTGACATTATGGGAAATATTTTGAAAAA
* *
6038378 GGTGACATTATGAGAATTATTTTGAAAAA
1 GGTGACATTATGGGAAATATTTTGAAAAA
*
6038407 GGTGACATTTTGGG-AAT-TTTTGAA
1 GGTGACATTATGGGAAATATTTTGAA
6038431 TGTAGACTAT
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
27 7 0.09
28 2 0.03
29 66 0.88
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (29 bp):
GGTGACATTATGGGAAATATTTTGAAAAA
Found at i:6040731 original size:22 final size:22
Alignment explanation
Indices: 6040706--6040763 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
6040696 TCGATTTTAT
** *
6040706 TTATTTATTTATTTCAAATTAG
1 TTATTTATTTATTTCAAAAAAA
* *
6040728 TTATTCATTTATTCCAAAAAAA
1 TTATTTATTTATTTCAAAAAAA
*
6040750 TTATTTAGTTATTT
1 TTATTTATTTATTT
6040764 TGAATTTATT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.55
Consensus pattern (22 bp):
TTATTTATTTATTTCAAAAAAA
Found at i:6040806 original size:23 final size:23
Alignment explanation
Indices: 6040748--6040806 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 23
6040738 ATTCCAAAAA
* ** *
6040748 AATTATTTAGTTATTTTGAATTT
1 AATTATTTATTTGGTTTGAAATT
* *
6040771 ATTTATTTGTTTGGTTTGAAATT
1 AATTATTTATTTGGTTTGAAATT
*
6040794 AATTGTTTATTTG
1 AATTATTTATTTG
6040807 AAAAGATATG
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.25, C:0.00, G:0.14, T:0.61
Consensus pattern (23 bp):
AATTATTTATTTGGTTTGAAATT
Found at i:6041258 original size:5 final size:5
Alignment explanation
Indices: 6041248--6041276 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
6041238 ATATATGTTT
6041248 ATTTA ATTTA ATTTA ATTTA ATTT- ATTTA
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA
6041277 TAATATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
ATTTA
Found at i:6041268 original size:15 final size:14
Alignment explanation
Indices: 6041245--6041277 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
6041235 TAAATATATG
6041245 TTTATTTAATTTAA
1 TTTATTTAATTTAA
6041259 TTTAATTTAATTT-A
1 TTT-ATTTAATTTAA
6041273 TTTAT
1 TTTAT
6041278 AATATTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.11
14 7 0.39
15 9 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTATTTAATTTAA
Found at i:6042684 original size:12 final size:12
Alignment explanation
Indices: 6042663--6042729 Score: 55
Period size: 12 Copynumber: 5.6 Consensus size: 12
6042653 TGGCCATGTA
*
6042663 GATGAGGGTGAT
1 GATGATGGTGAT
6042675 GATGATGGTGAT
1 GATGATGGTGAT
* *
6042687 GTTGATGGTGGT
1 GATGATGGTGAT
* * *
6042699 GGTGGTGGTGGT
1 GATGATGGTGAT
*
6042711 GATCA-GAGTGAT
1 GATGATG-GTGAT
6042723 GATGATG
1 GATGATG
6042730 CCCCCGAATA
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
11 1 0.02
12 41 0.95
13 1 0.02
ACGTcount: A:0.19, C:0.01, G:0.48, T:0.31
Consensus pattern (12 bp):
GATGATGGTGAT
Found at i:6042871 original size:33 final size:33
Alignment explanation
Indices: 6042834--6042898 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
6042824 ATTTGTAACT
* *
6042834 TTTTTAGTTATTCAAACTGA-ATTTTCTTTTTTC
1 TTTTTAATTAATCAAACT-ATATTTTCTTTTTTC
* *
6042867 TTTTTAATTAATCGAACTATTTTTTCTTTTTT
1 TTTTTAATTAATCAAACTATATTTTCTTTTTT
6042899 TTAAAATTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 1 0.04
33 26 0.96
ACGTcount: A:0.22, C:0.11, G:0.05, T:0.63
Consensus pattern (33 bp):
TTTTTAATTAATCAAACTATATTTTCTTTTTTC
Found at i:6045116 original size:75 final size:75
Alignment explanation
Indices: 6044999--6045146 Score: 287
Period size: 75 Copynumber: 2.0 Consensus size: 75
6044989 AAAAAATAAT
6044999 TAATGTGGATTTTTAATTTAATAACGCCGAAGGTTTGGGTTTGGTAATAGCTCGAATTGATTTGG
1 TAATGTGGATTTTTAATTTAATAACGCCGAAGGTTTGGGTTTGGTAATAGCTCGAATTGATTTGG
6045064 AGTTTTTTAA
66 AGTTTTTTAA
*
6045074 TAATGTGGATTTTTAATTTAATAACGCCGAATGTTTGGGTTTGGTAATAGCTCGAATTGATTTGG
1 TAATGTGGATTTTTAATTTAATAACGCCGAAGGTTTGGGTTTGGTAATAGCTCGAATTGATTTGG
6045139 AGTTTTTT
66 AGTTTTTT
6045147 TAACGACTGA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.26, C:0.07, G:0.24, T:0.44
Consensus pattern (75 bp):
TAATGTGGATTTTTAATTTAATAACGCCGAAGGTTTGGGTTTGGTAATAGCTCGAATTGATTTGG
AGTTTTTTAA
Found at i:6049552 original size:2 final size:2
Alignment explanation
Indices: 6049540--6049611 Score: 137
Period size: 2 Copynumber: 36.5 Consensus size: 2
6049530 TCTAGCTCTC
6049540 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6049581 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6049612 CTAAAAATTC
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 68 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6050804 original size:135 final size:135
Alignment explanation
Indices: 6050562--6050831 Score: 524
Period size: 135 Copynumber: 2.0 Consensus size: 135
6050552 TTTTTCCATC
6050562 CATATTCCAAATCATTATTCCTCAAGGAATAGTTTTTCCTTCACATCATATTTCCCCACCAATCA
1 CATATTCCAAATCATTATTCCTCAAGGAATAGTTTTTCCTTCACATCATATTTCCCCACCAATCA
6050627 CAATCCTTAAATCCTTCAAATTTCAACAAAAATTCTAATAATCAAGGTAGCTTTCTTCAGGGGTG
66 CAATCCTTAAATCCTTCAAATTTCAACAAAAATTCTAATAATCAAGGTAGCTTTCTTCAGGGGTG
6050692 TACAA
131 TACAA
6050697 CATATTCCAAATCATTATTCCTCAAGGAATAGTTTTTCCTTCACATCATATTTCCCCACCAATCA
1 CATATTCCAAATCATTATTCCTCAAGGAATAGTTTTTCCTTCACATCATATTTCCCCACCAATCA
6050762 CAATCCTTAAATCCTTCAAATTTCAACACAAAATTCT-ATAATCAAGGTAGCTTTCTTCAGGGGT
66 CAATCCTTAAATCCTTCAAATTTCAACA-AAAATTCTAATAATCAAGGTAGCTTTCTTCAGGGGT
6050826 GTACAA
130 GTACAA
6050832 TTTATTAATT
Statistics
Matches: 134, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
135 126 0.94
136 8 0.06
ACGTcount: A:0.34, C:0.25, G:0.08, T:0.33
Consensus pattern (135 bp):
CATATTCCAAATCATTATTCCTCAAGGAATAGTTTTTCCTTCACATCATATTTCCCCACCAATCA
CAATCCTTAAATCCTTCAAATTTCAACAAAAATTCTAATAATCAAGGTAGCTTTCTTCAGGGGTG
TACAA
Found at i:6052657 original size:191 final size:193
Alignment explanation
Indices: 6052333--6052715 Score: 752
Period size: 191 Copynumber: 2.0 Consensus size: 193
6052323 TTTAATTTTT
6052333 AATAGGTTGGGAAGGCAATTTAGCTAAGTGGATGAAAGATGGAGTGACTCTTCCGATTGTGGTAC
1 AATAGGTTGGGAAGGCAATTTAGCTAAGTGGATGAAAGATGGAGTGACTCTTCCGATTGTGGTAC
6052398 CAGACATGATCAAATGATTTATTGAATTAGTATCATAAATCAAATGACATAATTCAATTAGTGAA
66 CAGACATGATCAAATGATTTATTGAATTAGTATCATAAATCAAATGACATAATTCAATTAGTGAA
6052463 ATAAATTCAATTTTCATTAATGGAAAACTAA-TGAAAGTATATTAAGTTCTTTTT-AACGAAC
131 ATAAATTCAATTTTCATTAATGGAAAACTAATTGAAAGTATATTAAGTTCTTTTTAAACGAAC
6052524 AATAGGTTGGGAAGGCAATTTAGCTAAGTGGATGAAAGATGGAGTGACTCTTCCGATTGTGGTAC
1 AATAGGTTGGGAAGGCAATTTAGCTAAGTGGATGAAAGATGGAGTGACTCTTCCGATTGTGGTAC
6052589 CAGACATGATCAAATGATTTATTGAATTAGTATCATAAATCAAATGACATAATTCAATTAGTGAA
66 CAGACATGATCAAATGATTTATTGAATTAGTATCATAAATCAAATGACATAATTCAATTAGTGAA
6052654 ATAAATTCAATTTTCATTAATGGAAAACTAATTGAAAGTATATTAAGTTCTTTTTAAACGAA
131 ATAAATTCAATTTTCATTAATGGAAAACTAATTGAAAGTATATTAAGTTCTTTTTAAACGAA
6052716 ACAACTACTT
Statistics
Matches: 190, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
191 161 0.85
192 23 0.12
193 6 0.03
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (193 bp):
AATAGGTTGGGAAGGCAATTTAGCTAAGTGGATGAAAGATGGAGTGACTCTTCCGATTGTGGTAC
CAGACATGATCAAATGATTTATTGAATTAGTATCATAAATCAAATGACATAATTCAATTAGTGAA
ATAAATTCAATTTTCATTAATGGAAAACTAATTGAAAGTATATTAAGTTCTTTTTAAACGAAC
Found at i:6067762 original size:18 final size:18
Alignment explanation
Indices: 6067739--6067775 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
6067729 TTGACCGGTT
6067739 CCGACCCGACCCGTTGAC
1 CCGACCCGACCCGTTGAC
6067757 CCGACCCGACCCGTTGAC
1 CCGACCCGACCCGTTGAC
6067775 C
1 C
6067776 GTTGATCGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.51, G:0.22, T:0.11
Consensus pattern (18 bp):
CCGACCCGACCCGTTGAC
Found at i:6067905 original size:27 final size:27
Alignment explanation
Indices: 6067849--6067911 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
6067839 AAGGTGCTAT
* ** **
6067849 TTTTTGTAATTTTTTTAAAAAATGTTA
1 TTTTAGTAATTTTTGAAAAAAATGACA
*
6067876 TTTTCGTAATTTTTGAAAAAAATGACA
1 TTTTAGTAATTTTTGAAAAAAATGACA
6067903 TTTTAGTAA
1 TTTTAGTAA
6067912 ATATATTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.37, C:0.03, G:0.10, T:0.51
Consensus pattern (27 bp):
TTTTAGTAATTTTTGAAAAAAATGACA
Found at i:6067984 original size:2 final size:2
Alignment explanation
Indices: 6067977--6068006 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6067967 TAATTTTGTA
6067977 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6068007 TAATTTCGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6072109 original size:13 final size:13
Alignment explanation
Indices: 6072091--6072117 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6072081 AGCTATACGC
6072091 TAAGTTGAGCAAG
1 TAAGTTGAGCAAG
6072104 TAAGTTGAGCAAG
1 TAAGTTGAGCAAG
6072117 T
1 T
6072118 GTGAGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.30, T:0.26
Consensus pattern (13 bp):
TAAGTTGAGCAAG
Found at i:6074929 original size:166 final size:166
Alignment explanation
Indices: 6074655--6074998 Score: 652
Period size: 166 Copynumber: 2.1 Consensus size: 166
6074645 TTTTGAAACC
*
6074655 ACCATCGTGTTCGTTATCGAGTCAGGAACAATTCCCTTAAATTAATTGAGGTGAAACGCCGCCAA
1 ACCATCGTGTTCGTTATCGAGTCAGGAACAATTCCCTTAAATTAATTGAGGTGAAACACCGCCAA
* *
6074720 ACGCCGGGAATTTCAAGTCAAAGTCTCGACTTTTTTAGCATAATCGTAGATAAAATCTTAAATTC
66 ACGCCGGGAATTTCAAGTCAAAGTCTCGACTTTTTTAGCATAATCGCAGACAAAATCTTAAATTC
6074785 ACCGCCGATCGTTGCTCCGTTTTCGACACCTCCCGT
131 ACCGCCGATCGTTGCTCCGTTTTCGACACCTCCCGT
*
6074821 ACCATCGTGTTCGTTATCGAGTCAGGAACAATTCCCTTAAATTAATTGAGGTGAAACACTGCCAA
1 ACCATCGTGTTCGTTATCGAGTCAGGAACAATTCCCTTAAATTAATTGAGGTGAAACACCGCCAA
6074886 ACGCCGGGAATTTCAAGTCAAAGTCTCGACTTTTTTAGCATAATCGCAGACAAAATCTTAAATTC
66 ACGCCGGGAATTTCAAGTCAAAGTCTCGACTTTTTTAGCATAATCGCAGACAAAATCTTAAATTC
6074951 ACCGCCGATCGTTGCTCCGTTTTCGACACCTCCCGT
131 ACCGCCGATCGTTGCTCCGTTTTCGACACCTCCCGT
6074987 ACCATCGTGTTC
1 ACCATCGTGTTC
6074999 CTTGTGCCGT
Statistics
Matches: 174, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
166 174 1.00
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.29
Consensus pattern (166 bp):
ACCATCGTGTTCGTTATCGAGTCAGGAACAATTCCCTTAAATTAATTGAGGTGAAACACCGCCAA
ACGCCGGGAATTTCAAGTCAAAGTCTCGACTTTTTTAGCATAATCGCAGACAAAATCTTAAATTC
ACCGCCGATCGTTGCTCCGTTTTCGACACCTCCCGT
Found at i:6075352 original size:29 final size:29
Alignment explanation
Indices: 6075297--6075352 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
6075287 CCCGTTGACC
* * * *
6075297 GGTGACATTTTAGTAATTATTTTGAAACT
1 GGTGACATATTAGGAATTAATTCGAAACT
6075326 GGTGACATATTAGGAATTAATTCGAAA
1 GGTGACATATTAGGAATTAATTCGAAA
6075353 AGGGTGCTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.38
Consensus pattern (29 bp):
GGTGACATATTAGGAATTAATTCGAAACT
Found at i:6078563 original size:9 final size:9
Alignment explanation
Indices: 6078549--6078589 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
6078539 ATGGTCGTGC
6078549 TTTTAAATA
1 TTTTAAATA
6078558 TTTTAAAT-
1 TTTTAAATA
*
6078566 TTTTATATA
1 TTTTAAATA
*
6078575 ATTTAAATA
1 TTTTAAATA
6078584 TTTTAA
1 TTTTAA
6078590 TATAATTGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
8 7 0.26
9 20 0.74
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTTAAATA
Found at i:6078579 original size:17 final size:18
Alignment explanation
Indices: 6078549--6078596 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
6078539 ATGGTCGTGC
* *
6078549 TTTTAAATATTTTAAAT-
1 TTTTATATAATTTAAATA
6078566 TTTTATATAATTTAAATA
1 TTTTATATAATTTAAATA
6078584 TTTTAATATAATT
1 TTTT-ATATAATT
6078597 GTAGTTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 15 0.56
18 4 0.15
19 8 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTATATAATTTAAATA
Found at i:6082661 original size:19 final size:20
Alignment explanation
Indices: 6082624--6082661 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
6082614 GTTTCGTTCC
* *
6082624 AAAGAAAGGAAGGTTGAGAG
1 AAAGAAAGGAAGCTGGAGAG
6082644 AAAGAAA-GAAGCTGGAGA
1 AAAGAAAGGAAGCTGGAGA
6082662 AAAATAGGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.53, C:0.03, G:0.37, T:0.08
Consensus pattern (20 bp):
AAAGAAAGGAAGCTGGAGAG
Found at i:6089257 original size:21 final size:22
Alignment explanation
Indices: 6089227--6089297 Score: 81
Period size: 23 Copynumber: 3.2 Consensus size: 22
6089217 AAAACCCTAG
* * *
6089227 GGGGGTATCGATTCCCCT-ACA
1 GGGGGAATCGGTTCCCCTCAAA
6089248 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCC-TCAAA
**
6089271 GGGGGAATCGGTTCCCCTTTAA
1 GGGGGAATCGGTTCCCCTCAAA
6089293 GGGGG
1 GGGGG
6089298 GTATCAATTC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
21 15 0.35
22 9 0.21
23 19 0.44
ACGTcount: A:0.18, C:0.24, G:0.35, T:0.23
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCCTCAAA
Found at i:6089294 original size:22 final size:23
Alignment explanation
Indices: 6089247--6089298 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
6089237 ATTCCCCTAC
6089247 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
*
6089270 AGGGGGAATCGGTTCCCCTTTAA
1 AGGGGGAATCGGTTCCCCTTCAA
*
6089293 GGGGGG
1 AGGGGG
6089299 TATCAATTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.19, C:0.21, G:0.38, T:0.21
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:6089308 original size:23 final size:23
Alignment explanation
Indices: 6089225--6089309 Score: 77
Period size: 23 Copynumber: 3.8 Consensus size: 23
6089215 ATAAAACCCT
*
6089225 AGGGGGGTATCGATTCCCC--TA
1 AGGGGGGAATCGATTCCCCTTTA
* *
6089246 CA-GGGGGAATCGGTTCCCCTTCA
1 -AGGGGGGAATCGATTCCCCTTTA
* *
6089269 AAGGGGGAATCGGTTCCCCTTTA
1 AGGGGGGAATCGATTCCCCTTTA
* *
6089292 AGGGGGGTATCAATTCCC
1 AGGGGGGAATCGATTCCC
6089310 TCTGCACTAA
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
21 15 0.29
22 2 0.04
23 35 0.67
ACGTcount: A:0.20, C:0.25, G:0.32, T:0.24
Consensus pattern (23 bp):
AGGGGGGAATCGATTCCCCTTTA
Found at i:6098488 original size:30 final size:30
Alignment explanation
Indices: 6098452--6098522 Score: 142
Period size: 30 Copynumber: 2.4 Consensus size: 30
6098442 TCCGAAGGAC
6098452 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
6098482 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
6098512 CTATCCAGAGG
1 CTATCCAGAGG
6098523 CCCCGAAGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:6098541 original size:30 final size:30
Alignment explanation
Indices: 6098452--6098549 Score: 115
Period size: 30 Copynumber: 3.2 Consensus size: 30
6098442 TCCGAAGGAC
* *
6098452 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGCCACAAAGATCCTCGGTAA
* *
6098482 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGCCACAAAGATCCTCGGTAA
* * * *
6098512 CTATCCAGAGGCCCCGAAGAACCTAGGTAAA
1 CTATCCAGAGGCCACAAAGATCCTCGGT-AA
6098543 CTATCCA
1 CTATCCA
6098550 TATGTTCCTT
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
30 52 0.85
31 9 0.15
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (30 bp):
CTATCCAGAGGCCACAAAGATCCTCGGTAA
Found at i:6102742 original size:30 final size:30
Alignment explanation
Indices: 6102706--6102775 Score: 140
Period size: 30 Copynumber: 2.3 Consensus size: 30
6102696 CCCGAAGGAC
6102706 CTATCCAGAGGTCATAAAGATCCTCAGTAA
1 CTATCCAGAGGTCATAAAGATCCTCAGTAA
6102736 CTATCCAGAGGTCATAAAGATCCTCAGTAA
1 CTATCCAGAGGTCATAAAGATCCTCAGTAA
6102766 CTATCCAGAG
1 CTATCCAGAG
6102776 ACCCCGAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCAGTAA
Found at i:6103864 original size:64 final size:64
Alignment explanation
Indices: 6103712--6103868 Score: 160
Period size: 64 Copynumber: 2.5 Consensus size: 64
6103702 CAATGAAAGT
* * * ** *
6103712 ATGCATCGATGCACTA-CTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATCACTGGG
1 ATGCATCGATGCACTACCTG-TGCATCGATGCATAAAATGCATTCGATGTTCTATTATAAAAGAG
* * * *
6103776 ATGCATCGATGCA-TGCCTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATTTTAAAAG
1 ATGCATCGATGCACTACC-TGTGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTATAAAAG
6103839 AG
63 AG
6103841 -TGCATCGATGCACTACCTGTGCATCGAT
1 ATGCATCGATGCACTACCTGTGCATCGAT
6103869 ACACCTTCAA
Statistics
Matches: 76, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
63 1 0.01
64 60 0.79
65 15 0.20
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTGTGCATCGATGCATAAAATGCATTCGATGTTCTATTATAAAAGAG
Found at i:6106424 original size:20 final size:22
Alignment explanation
Indices: 6106399--6106438 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
6106389 AGTCGTGTAT
6106399 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
6106419 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
6106439 TCTGTAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:6107011 original size:20 final size:21
Alignment explanation
Indices: 6106986--6107060 Score: 80
Period size: 23 Copynumber: 3.5 Consensus size: 21
6106976 CTGTTGGAGC
*
6106986 CAGGGGTATTGATACCCAT-A
1 CAGGGGTATCGATACCCATCA
*
6107006 CAGGGGTATCGGTACCCATTCA
1 CAGGGGTATCGATACCCA-TCA
*
6107028 TAGGGGGTATCGATACCCATTCA
1 CA-GGGGTATCGATACCCA-TCA
*
6107051 TAGGGGTATC
1 CAGGGGTATC
6107061 AGTACCTCTT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
20 16 0.33
21 1 0.02
22 10 0.21
23 21 0.44
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (21 bp):
CAGGGGTATCGATACCCATCA
Found at i:6107037 original size:23 final size:22
Alignment explanation
Indices: 6107007--6107066 Score: 93
Period size: 23 Copynumber: 2.7 Consensus size: 22
6106997 ATACCCATAC
6107007 AGGGGTATCGGTACCCATTCAT
1 AGGGGTATCGGTACCCATTCAT
*
6107029 AGGGGGTATCGATACCCATTCAT
1 A-GGGGTATCGGTACCCATTCAT
*
6107052 AGGGGTATCAGTACC
1 AGGGGTATCGGTACC
6107067 TCTTAATATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 13 0.38
23 21 0.62
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (22 bp):
AGGGGTATCGGTACCCATTCAT
Found at i:6107309 original size:21 final size:19
Alignment explanation
Indices: 6107278--6107335 Score: 64
Period size: 18 Copynumber: 3.0 Consensus size: 19
6107268 AAATGTTTAA
*
6107278 TAAAAAAATACCAATTGTT
1 TAAAAAGATACCAATTGTT
*
6107297 TACAAAAGGATACTAATTG-T
1 TA-AAAA-GATACCAATTGTT
*
6107317 TAAAAAGATATCAATTGTT
1 TAAAAAGATACCAATTGTT
6107336 GGAAAATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
18 9 0.28
19 7 0.22
20 7 0.22
21 9 0.28
ACGTcount: A:0.48, C:0.09, G:0.10, T:0.33
Consensus pattern (19 bp):
TAAAAAGATACCAATTGTT
Found at i:6107850 original size:57 final size:57
Alignment explanation
Indices: 6107789--6107897 Score: 164
Period size: 57 Copynumber: 1.9 Consensus size: 57
6107779 TAAATTTAGG
** *
6107789 TCAAAAAATTTCAAATTTTGATATCAATTTTTAGAGAGATATCATTTGCATTTGAAA
1 TCAAAAAATTTCAAAAATTGATATCAATTGTTAGAGAGATATCATTTGCATTTGAAA
** *
6107846 TCAAAGTATTTGAAAAATTGATATCAATTGTTAGAGAGATATCATTTGCATT
1 TCAAAAAATTTCAAAAATTGATATCAATTGTTAGAGAGATATCATTTGCATT
6107898 AAAACCAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 46 1.00
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.39
Consensus pattern (57 bp):
TCAAAAAATTTCAAAAATTGATATCAATTGTTAGAGAGATATCATTTGCATTTGAAA
Found at i:6112167 original size:20 final size:19
Alignment explanation
Indices: 6112119--6112172 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 19
6112109 TAGTTTTCAG
6112119 AAAAAAAAAACAACATAATT
1 AAAAAAAAAACAACA-AATT
*
6112139 AAATAAAAAACAAC-AATT
1 AAAAAAAAAACAACAAATT
*
6112157 AAAAAACAAA-AACAAA
1 AAAAAAAAAACAACAAA
6112173 AAATTTTTCC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 3 0.10
18 14 0.47
20 13 0.43
ACGTcount: A:0.78, C:0.11, G:0.00, T:0.11
Consensus pattern (19 bp):
AAAAAAAAAACAACAAATT
Found at i:6112614 original size:23 final size:21
Alignment explanation
Indices: 6112583--6112640 Score: 73
Period size: 23 Copynumber: 2.7 Consensus size: 21
6112573 GTACCCATCT
6112583 AGGGGTATCGATACACATTCAA
1 AGGGGTATCGATACACATTC-A
6112605 AGAGGGTATCTG-TACACATTCA
1 AG-GGGTATC-GATACACATTCA
*
6112627 AGGTGTATCGATAC
1 AGGGGTATCGATAC
6112641 CTAGCAAGGG
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
20 1 0.03
21 9 0.28
22 5 0.16
23 16 0.50
24 1 0.03
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (21 bp):
AGGGGTATCGATACACATTCA
Found at i:6123983 original size:21 final size:20
Alignment explanation
Indices: 6123959--6124009 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
6123949 AAAATACCTC
6123959 AGTATCAATACT-AACCCTCTG
1 AGTATCAATACTGAACCC-C-G
* *
6123980 AGTATCGACACTGAACCCCG
1 AGTATCAATACTGAACCCCG
6124000 AGTATCAATA
1 AGTATCAATA
6124010 TTAAGAACAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 9 0.36
21 11 0.44
22 5 0.20
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (20 bp):
AGTATCAATACTGAACCCCG
Found at i:6124572 original size:202 final size:206
Alignment explanation
Indices: 6124226--6124634 Score: 781
Period size: 202 Copynumber: 2.0 Consensus size: 206
6124216 GCATGCTTTC
6124226 ATGAAGAAAAAAAACATACCATGAATGCACATATAATGACCTACATGTGGTATGATCAAGTTAGA
1 ATGAAGAAAAAAAACATACCATGAATGCACATATAATGACCTACATGTGGTATGATCAAGTTAGA
6124291 ATTGTGTTACCTTGAAGCTAGGTGACTGAAAAATATTTTTCAGTCAACAAGGTGAGTTTCTCCTT
66 ATTGTGTTACCTTGAAGCTAGGTGACTGAAAAATATTTTTCAGTCAACAAGGTGAGTTTCTCCTT
6124356 TCCCCTTGCCTTATAGCACTCCCTC-TCTCTTGCACTAATT-AAATCATGG-AA-AGTTATTAAC
131 TCCCCTTGCCTTATAGCACTCCCTCTTCTCTTGCACTAATTAAAATCATGGAAAGAGTTATTAAC
6124417 TCATTTTGGAA
196 TCATTTTGGAA
6124428 ATGAAGAAAAAAAACATACCATGAATGCACATATAATGACCTACATGTGGTATGATCAAGTTAGA
1 ATGAAGAAAAAAAACATACCATGAATGCACATATAATGACCTACATGTGGTATGATCAAGTTAGA
6124493 ATTGTGTTACCTTGAAGCTAGGTGACTGAAAAATATTTTTCAGTCAACAAGGTGAGTTTCTCCTT
66 ATTGTGTTACCTTGAAGCTAGGTGACTGAAAAATATTTTTCAGTCAACAAGGTGAGTTTCTCCTT
6124558 TCCCCTTGCCTTATAGCACTCCCTCTTCTCTTGCACTAATTAAAATCATGGAAATGAGTTATTAA
131 TCCCCTTGCCTTATAGCACTCCCTCTTCTCTTGCACTAATTAAAATCATGGAAA-GAGTTATTAA
6124623 CTCATTTTGGAA
195 CTCATTTTGGAA
6124635 CTTAAGAATG
Statistics
Matches: 202, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
202 155 0.77
203 15 0.07
204 9 0.04
205 2 0.01
207 21 0.10
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (206 bp):
ATGAAGAAAAAAAACATACCATGAATGCACATATAATGACCTACATGTGGTATGATCAAGTTAGA
ATTGTGTTACCTTGAAGCTAGGTGACTGAAAAATATTTTTCAGTCAACAAGGTGAGTTTCTCCTT
TCCCCTTGCCTTATAGCACTCCCTCTTCTCTTGCACTAATTAAAATCATGGAAAGAGTTATTAAC
TCATTTTGGAA
Found at i:6125372 original size:20 final size:19
Alignment explanation
Indices: 6125349--6125388 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
6125339 TTTTATCTTC
6125349 TTAATGTAATGTTTAATGGT
1 TTAATGTAATGTTT-ATGGT
*
6125369 TTAATTTAATGTTTATGGT
1 TTAATGTAATGTTTATGGT
6125388 T
1 T
6125389 CATTGTTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.55
Consensus pattern (19 bp):
TTAATGTAATGTTTATGGT
Found at i:6134098 original size:16 final size:16
Alignment explanation
Indices: 6134077--6134107 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
6134067 CTTAAAGGTT
6134077 TTATTTATTTTATTAG
1 TTATTTATTTTATTAG
6134093 TTATTTATTTTATTA
1 TTATTTATTTTATTA
6134108 ATTGTATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (16 bp):
TTATTTATTTTATTAG
Found at i:6134754 original size:13 final size:13
Alignment explanation
Indices: 6134736--6134765 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6134726 CTTTTCATTT
6134736 GGTTTTGAATTAG
1 GGTTTTGAATTAG
*
6134749 GGTTTTGATTTAG
1 GGTTTTGAATTAG
6134762 GGTT
1 GGTT
6134766 GAATATGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (13 bp):
GGTTTTGAATTAG
Found at i:6135001 original size:50 final size:50
Alignment explanation
Indices: 6134879--6135004 Score: 148
Period size: 50 Copynumber: 2.5 Consensus size: 50
6134869 AGGTTGGAAT
* * *
6134879 GATTT-TAGGTTAAAGTGGTATAGAGTTCGTTAAAGTGAAAATGGAGAAG
1 GATTTGTAGGTTAAAGTGGTTTAGGGTTCGTTAAAGTGAAAATGGACAAG
* * * * *
6134928 GATTTGTAGGTTAAAGTGATTTAGGGTT-TTTAATGTGAAAGTGGTCAAG
1 GATTTGTAGGTTAAAGTGGTTTAGGGTTCGTTAAAGTGAAAATGGACAAG
*
6134977 GGTTGTGTAGGTTAAAGTGGTTTAGGGT
1 GATT-TGTAGGTTAAAGTGGTTTAGGGT
6135005 AAGGTTCGAT
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
49 24 0.37
50 41 0.63
ACGTcount: A:0.29, C:0.02, G:0.33, T:0.36
Consensus pattern (50 bp):
GATTTGTAGGTTAAAGTGGTTTAGGGTTCGTTAAAGTGAAAATGGACAAG
Found at i:6135003 original size:25 final size:24
Alignment explanation
Indices: 6134930--6135004 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 24
6134920 TGGAGAAGGA
*
6134930 TTTGTAGGTTAAAGTGATTTAGGG
1 TTTGTAGGTTAAAGTGGTTTAGGG
* * * **
6134954 TTTTTAATGTGAAAGTGGTCAAGGG
1 TTTGT-AGGTTAAAGTGGTTTAGGG
6134979 TTGTGTAGGTTAAAGTGGTTTAGGG
1 TT-TGTAGGTTAAAGTGGTTTAGGG
6135004 T
1 T
6135005 AAGGTTCGAT
Statistics
Matches: 38, Mismatches: 11, Indels: 3
0.73 0.21 0.06
Matches are distributed among these distances:
24 4 0.11
25 32 0.84
26 2 0.05
ACGTcount: A:0.24, C:0.01, G:0.35, T:0.40
Consensus pattern (24 bp):
TTTGTAGGTTAAAGTGGTTTAGGG
Found at i:6142902 original size:2 final size:2
Alignment explanation
Indices: 6142897--6142930 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
6142887 TATTTTAATA
*
6142897 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6142931 TTAATCTGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6142910 original size:10 final size:10
Alignment explanation
Indices: 6142883--6142930 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
6142873 ATAATCAAAT
* *
6142883 AATATATTTT
1 AATATATATA
6142893 AATAATATATA
1 AAT-ATATATA
6142904 AATATATATA
1 AATATATATA
*
6142914 TATATATATA
1 AATATATATA
*
6142924 TATATAT
1 AATATAT
6142931 TTAATCTGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
10 26 0.76
11 8 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
AATATATATA
Found at i:6145528 original size:19 final size:18
Alignment explanation
Indices: 6145495--6145530 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
6145485 CTTATTAATC
6145495 TAATATTATTATAAATAA
1 TAATATTATTATAAATAA
*
6145513 TAATATATATTTTAAATA
1 TAATAT-TATTATAAATA
6145531 CTCTTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAATATTATTATAAATAA
Found at i:6149792 original size:160 final size:155
Alignment explanation
Indices: 6149523--6149835 Score: 581
Period size: 160 Copynumber: 2.0 Consensus size: 155
6149513 CTATGAATGC
6149523 ATTACTGGCTGCATTGGCCATAATACATTAAGAATAGGGCACTATTCAAGGAAAACCATTGAGTA
1 ATTACTGGCTGCATTGGCCATAATACATTAAGAATAGGGCACTATTCAAGGAAAACCATTGAGTA
6149588 TTAATTGACATGGCAGTACACACATTTTCTTGACTCCTAAATGGGTTGATGCTGGCATACAGGTT
66 TTAATTGACATGGCAGTACACACATTTTCTTGACTCCTAAATGGGTTGATGCTGGCATACAGGTT
6149653 AATATTGCTTATCATTTTTACTGCT
131 AATATTGCTTATCATTTTTACTGCT
6149678 ATTACTGGCTGCATTGGCCATAATACATTAAGAATCTAGGGCACTATTCAAGGAAAACCATTGAG
1 ATTACTGGCTGCATTGGCCATAATACATTAAGAA--TAGGGCACTATTCAAGGAAAACCATTGAG
6149743 TATCTTAATTGACAGTGGCAGTACACACATTTTCTTGACTCCTAAATGGGTTGATGCTGGCATAC
64 TA--TTAATTGACA-TGGCAGTACACACATTTTCTTGACTCCTAAATGGGTTGATGCTGGCATAC
6149808 AGGTTAATATTGCTTATCATTTTTACTG
126 AGGTTAATATTGCTTATCATTTTTACTG
6149836 TGGCTAATGG
Statistics
Matches: 153, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
155 34 0.22
157 31 0.20
159 10 0.07
160 78 0.51
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (155 bp):
ATTACTGGCTGCATTGGCCATAATACATTAAGAATAGGGCACTATTCAAGGAAAACCATTGAGTA
TTAATTGACATGGCAGTACACACATTTTCTTGACTCCTAAATGGGTTGATGCTGGCATACAGGTT
AATATTGCTTATCATTTTTACTGCT
Found at i:6158810 original size:23 final size:23
Alignment explanation
Indices: 6158771--6158837 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
6158761 CACCACAGCT
* *
6158771 CGTATAAATGCATCGAAGTGCCA
1 CGTAAAAATGCACCGAAGTGCCA
* * *
6158794 CGTAGAATTGTACCGAAGTGCCA
1 CGTAAAAATGCACCGAAGTGCCA
6158817 CGTAAAAATGCACCGAAGTGC
1 CGTAAAAATGCACCGAAGTGC
6158838 TATATAAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.19
Consensus pattern (23 bp):
CGTAAAAATGCACCGAAGTGCCA
Found at i:6161964 original size:23 final size:23
Alignment explanation
Indices: 6161936--6162004 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
6161926 CACCACAGCT
6161936 CGTATAAATGCACCGAAGTGCCA
1 CGTATAAATGCACCGAAGTGCCA
* * * *
6161959 CTTATAATTGCACCGTAGTGCCG
1 CGTATAAATGCACCGAAGTGCCA
*
6161982 CGTAAAAATGCACCGAAGTGCCA
1 CGTATAAATGCACCGAAGTGCCA
6162005 TATAAGGTTG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.20
Consensus pattern (23 bp):
CGTATAAATGCACCGAAGTGCCA
Found at i:6162402 original size:2 final size:2
Alignment explanation
Indices: 6162395--6162440 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
6162385 ATGTCTTATC
6162395 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6162437 AT AT
1 AT AT
6162441 TCACATGTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6162509 original size:2 final size:2
Alignment explanation
Indices: 6162502--6162545 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
6162492 ATTCATCTTC
6162502 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6162544 AT
1 AT
6162546 CATTTTTCCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6163338 original size:20 final size:18
Alignment explanation
Indices: 6163310--6163358 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
6163300 TGAAATACAT
*
6163310 ATACAATAACATGTCAACAC
1 ATAC-ATAACATAT-AACAC
*
6163330 ATACTATAACATATAACTC
1 ATAC-ATAACATATAACAC
6163349 ATACATAACA
1 ATACATAACA
6163359 AACACATGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 6 0.23
19 8 0.31
20 12 0.46
ACGTcount: A:0.51, C:0.22, G:0.02, T:0.24
Consensus pattern (18 bp):
ATACATAACATATAACAC
Found at i:6163768 original size:64 final size:64
Alignment explanation
Indices: 6163661--6163798 Score: 181
Period size: 64 Copynumber: 2.2 Consensus size: 64
6163651 TTCTCTTGAA
*
6163661 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACATTCGATGTTTTCA-TTTTAAGGGG
1 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAA-GGG
* * * ** *
6163725 GTGCATCGATGCACT-CCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCATTTTTAATGG
1 GTGCATCGATGCACTACC-CATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAAGGG
6163789 GTGCATCGAT
1 GTGCATCGAT
6163799 ACACATTGAA
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
63 2 0.03
64 57 0.88
65 6 0.09
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (64 bp):
GTGCATCGATGCACTACCCATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAAGGG
Found at i:6165860 original size:17 final size:17
Alignment explanation
Indices: 6165830--6165869 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
6165820 AAAAAAATTT
* * *
6165830 AACAATAAATTAATCTA
1 AACAAAAAAATAATCGA
6165847 AACAAAAAAATAATCGA
1 AACAAAAAAATAATCGA
6165864 AACAAA
1 AACAAA
6165870 TAAACTCACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.68, C:0.12, G:0.03, T:0.17
Consensus pattern (17 bp):
AACAAAAAAATAATCGA
Found at i:6173329 original size:20 final size:20
Alignment explanation
Indices: 6173306--6173359 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
6173296 AACGCGATTT
*
6173306 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
6173326 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
6173346 AGAAAATCGCAACG
1 AGAAAATCGCAACG
6173360 CGAGCTTCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.52, C:0.19, G:0.19, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:6173419 original size:20 final size:20
Alignment explanation
Indices: 6173394--6173579 Score: 228
Period size: 20 Copynumber: 9.2 Consensus size: 20
6173384 TTTAGAAGAA
*
6173394 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGAGAG
* *
6173414 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAG
* *
6173434 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAG
6173454 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAG
* * *
6173474 AGTCGCAACGCGATTTAGAAGAA
1 AATCGCAATGCGA-TT-G-AGAG
* *
6173497 AATCGCAATGTGACTGAGAG
1 AATCGCAATGCGATTGAGAG
*
6173517 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
* *
6173537 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAG
6173557 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAG
6173577 AAT
1 AAT
6173580 AGAATCGCAA
Statistics
Matches: 146, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
20 128 0.88
21 3 0.02
22 2 0.01
23 13 0.09
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (20 bp):
AATCGCAATGCGATTGAGAG
Found at i:6173501 original size:83 final size:83
Alignment explanation
Indices: 6173414--6173571 Score: 217
Period size: 83 Copynumber: 1.9 Consensus size: 83
6173404 CGATTGATAG
* * * * * * *
6173414 AATCGCAATGCGATTTATAGAATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAGTCG
1 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATCG
6173479 CAACGCGATTTAGAAGAA
66 CAACGCGATTTAGAAGAA
* * *
6173497 AATCGCAATGTGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAATCG
1 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATCG
*
6173562 CAATGCGATT
66 CAACGCGATT
6173572 GAGAGAATAG
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
83 64 1.00
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.23
Consensus pattern (83 bp):
AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATCG
CAACGCGATTTAGAAGAA
Found at i:6173505 original size:103 final size:103
Alignment explanation
Indices: 6173373--6173577 Score: 356
Period size: 103 Copynumber: 2.0 Consensus size: 103
6173363 GCTTCCAAGT
* * * * *
6173373 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTTATAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
6173438 GCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAG
66 GCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAG
*
6173476 TCGCAACGCGATTTAGAAGAAAATCGCAATGTGACTGAGAGAATCGCAATGCGACTGAGAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
6173541 GCAATGCGATTTATAGAATCGCAATGCGATTGAGAGA
66 GCAATGCGATTTATAGAATCGCAATGCGATTGAGAGA
6173578 ATAGAATCGC
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 96 1.00
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.22
Consensus pattern (103 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
GCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAG
Found at i:6173607 original size:20 final size:20
Alignment explanation
Indices: 6173582--6173625 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
6173572 GAGAGAATAG
**
6173582 AATCGCAACGTTAAAAAGAA
1 AATCGCAACGCAAAAAAGAA
*
6173602 AATCGCAACGCAAAAAATAA
1 AATCGCAACGCAAAAAAGAA
6173622 AATC
1 AATC
6173626 AAAAGAATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.57, C:0.18, G:0.11, T:0.14
Consensus pattern (20 bp):
AATCGCAACGCAAAAAAGAA
Found at i:6174400 original size:6 final size:6
Alignment explanation
Indices: 6174391--6174457 Score: 134
Period size: 6 Copynumber: 11.2 Consensus size: 6
6174381 CCGTCTCGTC
6174391 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
6174439 TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG T
6174458 AATACGTGTC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 61 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.34
Consensus pattern (6 bp):
TCGTGG
Found at i:6174587 original size:20 final size:20
Alignment explanation
Indices: 6174562--6174732 Score: 189
Period size: 20 Copynumber: 8.4 Consensus size: 20
6174552 ATTTTCAACG
*
6174562 TTGCGATTCTATAAATCGTA
1 TTGCGATTCTATAAATCGCA
* * *
6174582 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTATAAATCGCA
* * *
6174602 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTATAAATCGCA
* *
6174622 TTGCGATTTTCTTCTAAATCGCG
1 TTGCGA--TTC-TATAAATCGCA
* * *
6174645 TTGCGACTCTCTCAATCGCA
1 TTGCGATTCTATAAATCGCA
*
6174665 TTGCGATTATATAAATCGCA
1 TTGCGATTCTATAAATCGCA
6174685 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTATAAATCGCA
*
6174705 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTATAAATCGCA
6174725 TTGCGATT
1 TTGCGATT
6174733 TTCTTCTAAA
Statistics
Matches: 132, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
20 113 0.86
21 2 0.02
22 3 0.02
23 14 0.11
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (20 bp):
TTGCGATTCTATAAATCGCA
Found at i:6174704 original size:83 final size:83
Alignment explanation
Indices: 6174560--6174712 Score: 207
Period size: 83 Copynumber: 1.8 Consensus size: 83
6174550 CGATTTTCAA
* * * * * * * * *
6174560 CGTTGCGATTCTATAAATCGTATTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCATTG
1 CGTTGCGACTCTATAAATCGCATTGCGATTATATAAATCGCATTGCGATTCTATAAATCGCATTG
6174625 CGATTTTCTTCTAAATCG
66 CGATTTTCTTCTAAATCG
* *
6174643 CGTTGCGACTCTCTCAATCGCATTGCGATTATATAAATCGCATTGCGATTCTATAAATCGCATTG
1 CGTTGCGACTCTATAAATCGCATTGCGATTATATAAATCGCATTGCGATTCTATAAATCGCATTG
6174708 CGATT
66 CGATT
6174713 CTATCAATCG
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
83 59 1.00
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.37
Consensus pattern (83 bp):
CGTTGCGACTCTATAAATCGCATTGCGATTATATAAATCGCATTGCGATTCTATAAATCGCATTG
CGATTTTCTTCTAAATCG
Found at i:6174741 original size:103 final size:103
Alignment explanation
Indices: 6174562--6174753 Score: 321
Period size: 103 Copynumber: 1.9 Consensus size: 103
6174552 ATTTTCAACG
* * * * * * *
6174562 TTGCGATTCTATAAATCGTATTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCATTGCG
1 TTGCGATTATATAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTGCG
6174627 ATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCA
66 ATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCA
6174665 TTGCGATTATATAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTGCG
1 TTGCGATTATATAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTGCG
6174730 ATTTTCTTCTAAATCGCGTTGCGA
66 ATTTTCTTCTAAATCGCGTTGCGA
6174754 ACTTGGAAGC
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 82 1.00
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.37
Consensus pattern (103 bp):
TTGCGATTATATAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTGCG
ATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCA
Found at i:6174830 original size:20 final size:20
Alignment explanation
Indices: 6174560--6174857 Score: 134
Period size: 20 Copynumber: 14.6 Consensus size: 20
6174550 CGATTTTCAA
* *
6174560 CGTTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
** * * *
6174580 TATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
6174600 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
6174620 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
6174643 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
6174663 CATTGCGATTATATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
6174683 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
6174703 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
6174723 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
6174746 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
6174767 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
6174785 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
6174807 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
6174827 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
6174846 CGTTGCGATTTT
1 CGTTGCGATTTT
6174858 ATTGGTCATT
Statistics
Matches: 223, Mismatches: 44, Indels: 23
0.77 0.15 0.08
Matches are distributed among these distances:
18 2 0.01
19 17 0.08
20 156 0.70
21 14 0.06
22 6 0.03
23 28 0.13
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:6174847 original size:19 final size:20
Alignment explanation
Indices: 6174807--6174857 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
6174797 TTCTTTTTAA
*
6174807 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
6174827 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
6174846 CGTTGCGATTTT
1 CGTTGCGATTTT
6174858 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:6177695 original size:16 final size:16
Alignment explanation
Indices: 6177663--6177694 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
6177653 TCATTTTAAA
6177663 ATTTAAATATATATAT
1 ATTTAAATATATATAT
6177679 ATTT-AATATATA-AT
1 ATTTAAATATATATAT
6177693 AT
1 AT
6177695 AGATAGATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.25
15 8 0.50
16 4 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTAAATATATATAT
Found at i:6178132 original size:14 final size:14
Alignment explanation
Indices: 6178113--6178140 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6178103 AGTCCGACTC
6178113 ATCCTCGTCAATTT
1 ATCCTCGTCAATTT
6178127 ATCCTCGTCAATTT
1 ATCCTCGTCAATTT
6178141 TTATATTTTT
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:0.21, C:0.29, G:0.07, T:0.43
Consensus pattern (14 bp):
ATCCTCGTCAATTT
Found at i:6179556 original size:25 final size:24
Alignment explanation
Indices: 6179528--6179574 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
6179518 TTTAGTAGAA
*
6179528 TTAAGGTTTTTAAATAAAAAAATAT
1 TTAAAGTTTTTAAA-AAAAAAATAT
* *
6179553 TTAAATTTTTTAAAAATAAAAT
1 TTAAAGTTTTTAAAAAAAAAAT
6179575 TTAAAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 7 0.37
25 12 0.63
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (24 bp):
TTAAAGTTTTTAAAAAAAAAATAT
Found at i:6179784 original size:18 final size:19
Alignment explanation
Indices: 6179763--6179798 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
6179753 ATAATTATTA
*
6179763 ATTTATAA-AATTTTATAT
1 ATTTATAATAATATTATAT
6179781 ATTTATAATAATATTATA
1 ATTTATAATAATATTATA
6179799 ATGGTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTATAATAATATTATAT
Found at i:6182632 original size:18 final size:17
Alignment explanation
Indices: 6182584--6182639 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
6182574 AATACTAAAC
6182584 AAATT-AAATAAA-TAA
1 AAATTAAAATAAATTAA
6182599 AATATTAACAAT-AATTAA
1 AA-ATTAA-AATAAATTAA
*
6182617 AAATTAAAATAGAATTTA
1 AAATTAAAATA-AATTAA
6182635 AAATT
1 AAATT
6182640 CTTATCGTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
15 2 0.06
16 6 0.18
17 8 0.24
18 18 0.53
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (17 bp):
AAATTAAAATAAATTAA
Found at i:6182733 original size:12 final size:13
Alignment explanation
Indices: 6182716--6182757 Score: 52
Period size: 12 Copynumber: 3.2 Consensus size: 13
6182706 TTATAACTGC
6182716 AAAAATTAATA-A
1 AAAAATTAATATA
6182728 AAAAATTAATATA
1 AAAAATTAATATA
6182741 ATAAAATTTAAT-TA
1 A-AAAA-TTAATATA
6182755 AAA
1 AAA
6182758 TAATAAATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 11 0.41
13 4 0.15
14 7 0.26
15 5 0.19
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAAATTAATATA
Found at i:6182755 original size:19 final size:20
Alignment explanation
Indices: 6182731--6182783 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
6182721 TTAATAAAAA
6182731 AATTAATATAATAAAAT-TT
1 AATTAATATAATAAAATGTT
* *
6182750 AATTAAAATAATAAATTGTT
1 AATTAATATAATAAAATGTT
*
6182770 AATGTATTATAATA
1 AAT-TAATATAATA
6182784 CAATAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 15 0.54
20 5 0.18
21 8 0.29
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (20 bp):
AATTAATATAATAAAATGTT
Found at i:6186618 original size:42 final size:42
Alignment explanation
Indices: 6186571--6186658 Score: 104
Period size: 42 Copynumber: 2.1 Consensus size: 42
6186561 GATTTATTTT
* * ** * *
6186571 TTTGTTTCACGTGATTTATTTTTTGAAAAATATTTTTTCGTG
1 TTTGTTTCACGTAATTCATTTACTGAAAAATATTTTCTAGTG
* *
6186613 TTTGTTTTATGTAATTCATTTACTGAAAAATATTTTCTAGTG
1 TTTGTTTCACGTAATTCATTTACTGAAAAATATTTTCTAGTG
6186655 TTTG
1 TTTG
6186659 GTTGGAGAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.24, C:0.07, G:0.14, T:0.56
Consensus pattern (42 bp):
TTTGTTTCACGTAATTCATTTACTGAAAAATATTTTCTAGTG
Found at i:6186795 original size:27 final size:28
Alignment explanation
Indices: 6186757--6186816 Score: 113
Period size: 27 Copynumber: 2.2 Consensus size: 28
6186747 TATAAGTCAT
6186757 TTTTAATGAATTTAATA-TAATAAAATA
1 TTTTAATGAATTTAATATTAATAAAATA
6186784 TTTTAATGAATTTAATATTAATAAAATA
1 TTTTAATGAATTTAATATTAATAAAATA
6186812 TTTTA
1 TTTTA
6186817 TAAAATATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 17 0.53
28 15 0.47
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (28 bp):
TTTTAATGAATTTAATATTAATAAAATA
Found at i:6186821 original size:12 final size:13
Alignment explanation
Indices: 6186774--6186839 Score: 71
Period size: 14 Copynumber: 4.9 Consensus size: 13
6186764 GAATTTAATA
6186774 TAATAAAATATTT
1 TAATAAAATATTT
** *
6186787 TAATGAATTTAATAT
1 TAAT-AAAAT-ATTT
6186802 TAATAAAATATTT
1 TAATAAAATATTT
6186815 T-ATAAAATATTT
1 TAATAAAATATTT
6186827 TAATCAAAATATT
1 TAAT-AAAATATT
6186840 AATATAATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
12 12 0.28
13 10 0.23
14 14 0.33
15 7 0.16
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (13 bp):
TAATAAAATATTT
Found at i:6186841 original size:12 final size:12
Alignment explanation
Indices: 6186774--6186848 Score: 55
Period size: 12 Copynumber: 5.8 Consensus size: 12
6186764 GAATTTAATA
6186774 TAATAAAATATTT
1 TAATAAAATA-TT
6186787 TAATGAATTTAATA-T
1 TAAT-AA---AATATT
6186802 TAATAAAATATT
1 TAATAAAATATT
*
6186814 TTATAAAATATTT
1 TAATAAAATA-TT
6186827 TAATCAAAATA-T
1 TAAT-AAAATATT
*
6186839 TAATATAATA
1 TAATAAAATA
6186849 AATATAATTA
Statistics
Matches: 52, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
11 9 0.17
12 15 0.29
13 9 0.17
14 10 0.19
15 5 0.10
17 4 0.08
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (12 bp):
TAATAAAATATT
Found at i:6186848 original size:25 final size:25
Alignment explanation
Indices: 6186774--6186908 Score: 62
Period size: 25 Copynumber: 5.3 Consensus size: 25
6186764 GAATTTAATA
** *
6186774 TAATAAAATATTTTAATGAATTTAATAT
1 TAATAAAATA-TTTAAT-AAAAT-ATTT
*
6186802 TAATAAAATATTTTATAAAATATTT
1 TAATAAAATATTTAATAAAATATTT
* * *
6186827 TAATCAAAATA-TTAATATAATAAATA
1 TAAT-AAAATATTTAATAAAAT-ATTT
* * * *
6186853 TAATTAAATATAT-ATATAATTTTAT
1 TAATAAAATATTTAATAAAATATT-T
* *
6186878 TTATAATAATATATAAT-AAAT-TTT
1 TAATAA-AATATTTAATAAAATATTT
6186902 TAATAAA
1 TAATAAA
6186909 TTTATATTAT
Statistics
Matches: 84, Mismatches: 17, Indels: 17
0.71 0.14 0.14
Matches are distributed among these distances:
23 1 0.01
24 7 0.08
25 33 0.39
26 26 0.31
27 7 0.08
28 10 0.12
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (25 bp):
TAATAAAATATTTAATAAAATATTT
Found at i:6186907 original size:24 final size:26
Alignment explanation
Indices: 6186859--6186907 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
6186849 AATATAATTA
* *
6186859 AATATATATATAATTTTATTTATAAT
1 AATATATATATAAATTTATTAATAAT
6186885 AATATATA-ATAAATTT-TTAATAA
1 AATATATATATAAATTTATTAATAA
6186908 ATTTATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.29
25 7 0.33
26 8 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
AATATATATATAAATTTATTAATAAT
Found at i:6186955 original size:27 final size:25
Alignment explanation
Indices: 6186882--6186973 Score: 78
Period size: 27 Copynumber: 3.5 Consensus size: 25
6186872 TTTTATTTAT
* *
6186882 AATAATATATAATAAATTTTTAATAA
1 AATAATAT-TATTAAATTATTAATAA
* * *
6186908 ATTTATATTATT-TATTAATTACATAGA
1 AATAATATTATTAAATT-ATTA-ATA-A
6186935 AATAATATTATTAAATTATTAATAA
1 AATAATATTATTAAATTATTAATAA
6186960 TGAATAATATTATT
1 --AATAATATTATT
6186974 TGTATATTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
24 3 0.06
25 7 0.13
26 12 0.23
27 27 0.52
28 3 0.06
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (25 bp):
AATAATATTATTAAATTATTAATAA
Found at i:6187031 original size:23 final size:23
Alignment explanation
Indices: 6187012--6187056 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
6187002 AATAATATTT
*
6187012 TAATAAAGATATTTAAAATATAC
1 TAATAAACATATTTAAAATATAC
* *
6187035 TAATTAACATTTTTAAAATATA
1 TAATAAACATATTTAAAATATA
6187057 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (23 bp):
TAATAAACATATTTAAAATATAC
Found at i:6187653 original size:32 final size:32
Alignment explanation
Indices: 6187617--6187679 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
6187607 TTTGGTGGTA
6187617 TTTGTTGATTTAACGTTTGAAAGTCACATTCG
1 TTTGTTGATTTAACGTTTGAAAGTCACATTCG
* *
6187649 TTTGTTGATTTAACGTTTGAGAGTCGCATTC
1 TTTGTTGATTTAACGTTTGAAAGTCACATTC
6187680 ATGGTCTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.22, C:0.13, G:0.21, T:0.44
Consensus pattern (32 bp):
TTTGTTGATTTAACGTTTGAAAGTCACATTCG
Found at i:6188414 original size:223 final size:226
Alignment explanation
Indices: 6188001--6188444 Score: 634
Period size: 223 Copynumber: 2.0 Consensus size: 226
6187991 CACGTATTCT
* * * *
6188001 ATTATTTCTTTAAATTATTGGGTACTCTATCATTACCTAAATCTTGTATATCACTCACCTCTCTC
1 ATTATTTATTTAAATTATTAGGTACTCCATCATTACCTAAACCTTGTATATCACTCACCTCTCTC
* *
6188066 ATATAAATAACATCGTCAATAAACATAAAATCACACCAAAATTTAATTTCATATTTATTGTTCTA
66 ATATAAATAACATCGTCAATAAACATAAAATAACACCAAAATTTAA-TT-ATATTTATTATTCTA
*
6188131 TAATTTTCTCTATTAAGCTAAGTAGATTTTGTTATAGTTTTTAGAAAGTAAAATTAATTTTTATT
129 TAATTTTCTCTATCAAGCTAAGTAGATTTTGTTATAGTTTTTAGAAAGTAAAATTAATTTTTATT
6188196 ATTTTATTGTCATTTTAAATTTAATTTCCTTAA
194 ATTTTATTGTCATTTTAAATTTAATTTCCTTAA
* *
6188229 ATTATTTATTTAAATTATTAGGTACTCCATCATTA-CTCGAACCTTGTGA-ATCAGTCACC-CTC
1 ATTATTTATTTAAATTATTAGGTACTCCATCATTACCT-AAACCTTGT-ATATCACTCACCTCTC
* *
6188291 -CTATATAAATAGCATCGTCAATAAACATAAAATAACACTAAAATTTAA-T-TA-TTATTCATTC
64 TC-ATATAAATAACATCGTCAATAAACATAAAATAACACCAAAATTTAATTATATTTATT-ATTC
* ** *
6188352 TATAATTTTTCTTTATCAATTTAAGTAGATTTT-TTATAGTTTTTAGAAGGTAAAATTAATTTTT
127 TATAA-TTTTCTCTATCAAGCTAAGTAGATTTTGTTATAGTTTTTAGAAAGTAAAATTAATTTTT
6188416 ATTATTTTATTGTCATTTTAAATTTAATT
191 ATTATTTTATTGTCATTTTAAATTTAATT
6188445 ATTTGATTAA
Statistics
Matches: 196, Mismatches: 15, Indels: 15
0.87 0.07 0.07
Matches are distributed among these distances:
222 5 0.03
223 69 0.35
224 23 0.12
225 1 0.01
226 1 0.01
227 48 0.24
228 48 0.24
229 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (226 bp):
ATTATTTATTTAAATTATTAGGTACTCCATCATTACCTAAACCTTGTATATCACTCACCTCTCTC
ATATAAATAACATCGTCAATAAACATAAAATAACACCAAAATTTAATTATATTTATTATTCTATA
ATTTTCTCTATCAAGCTAAGTAGATTTTGTTATAGTTTTTAGAAAGTAAAATTAATTTTTATTAT
TTTATTGTCATTTTAAATTTAATTTCCTTAA
Found at i:6201000 original size:77 final size:76
Alignment explanation
Indices: 6200874--6201028 Score: 292
Period size: 77 Copynumber: 2.0 Consensus size: 76
6200864 CATGCTTTGA
*
6200874 TGCTTACCTTTCTTAACATCGATTTACCTTTATCACTATTTGCCATATGATTTTTAGTATTGAAA
1 TGCTTACCTTTCTTAACATCAATTTACCTTTATCACTATTTGCCATATGATTTTTAGTATTGAAA
6200939 TTTGGCAAAAC
66 TTTGGCAAAAC
6200950 TGCTTACCTTTCTTAACATCAATTTTACCTTTATCACTATTTGCCATATGATTTTTAGTATTGAA
1 TGCTTACCTTTCTTAACATCAA-TTTACCTTTATCACTATTTGCCATATGATTTTTAGTATTGAA
6201015 ATTTGGCAAAAC
65 ATTTGGCAAAAC
6201027 TG
1 TG
6201029 TCGAGATAAT
Statistics
Matches: 77, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
76 21 0.27
77 56 0.73
ACGTcount: A:0.28, C:0.18, G:0.10, T:0.44
Consensus pattern (76 bp):
TGCTTACCTTTCTTAACATCAATTTACCTTTATCACTATTTGCCATATGATTTTTAGTATTGAAA
TTTGGCAAAAC
Found at i:6203701 original size:14 final size:14
Alignment explanation
Indices: 6203682--6204366 Score: 225
Period size: 14 Copynumber: 47.8 Consensus size: 14
6203672 CTTGAGTACA
*
6203682 TATTTAATAATAAT
1 TATTTAATATTAAT
6203696 TATTTAAGT-TTAAT
1 TATTTAA-TATTAAT
* *
6203710 GATTTAATAATAAT
1 TATTTAATATTAAT
*
6203724 TACTTAACT-TTAAT
1 TATTTAA-TATTAAT
*
6203738 GATTTAACT-TTAAT
1 TATTTAA-TATTAAT
* *
6203752 GATTTAATAATAAT
1 TATTTAATATTAAT
*
6203766 TACTTAACT-TTAAT
1 TATTTAA-TATTAAT
*
6203780 GATTTAACT-TTAAT
1 TATTTAA-TATTAAT
* * *
6203794 GATTTGATAATAAT
1 TATTTAATATTAAT
*
6203808 TACTTAACT-TTAAT
1 TATTTAA-TATTAAT
*
6203822 GATTTAA-ATCTAAT
1 TATTTAATAT-TAAT
* *
6203836 GATTTAATAATAAT
1 TATTTAATATTAAT
* *
6203850 TACTTAACT-TTAAA
1 TATTTAA-TATTAAT
6203864 TATTTAACT-TTAAT
1 TATTTAA-TATTAAT
* *
6203878 GATTTAATAATAAT
1 TATTTAATATTAAT
*
6203892 TACTTAACT-TTAAT
1 TATTTAA-TATTAAT
*
6203906 GATTTAACT-TTAAT
1 TATTTAA-TATTAAT
* *
6203920 AATTTAATAATAAT
1 TATTTAATATTAAT
*
6203934 TACTTAACT-TTAAT
1 TATTTAA-TATTAAT
*
6203948 GATTTAA-ATTTAAT
1 TATTTAATA-TTAAT
* * *
6203962 AATTTAATAATATT
1 TATTTAATATTAAT
*
6203976 TATTTAATTTTAAT
1 TATTTAATATTAAT
* *
6203990 TGGTTTAATAATAAT
1 T-ATTTAATATTAAT
6204005 TATTTAAGT-TTAAT
1 TATTTAA-TATTAAT
*
6204019 GATTTAA-ATTTAAT
1 TATTTAATA-TTAAT
* *
6204033 AATTTAATAATAAT
1 TATTTAATATTAAT
6204047 TATTTAAGT-TTAAT
1 TATTTAA-TATTAAT
* *
6204061 GATTTAA-ATTTAAC
1 TATTTAATA-TTAAT
* *
6204075 GATTTAATAATAAT
1 TATTTAATATTAAT
6204089 TATTTAATGATTTAACTTT
1 TATTTAAT-A-TTAA---T
*
6204108 AATGATTTAATAATAAT
1 --T-ATTTAATATTAAT
* *
6204125 TACTTAATTTTTAAT
1 TATTTAA-TATTAAT
*
6204140 GATTTAA-ATTTAAT
1 TATTTAATA-TTAAT
* *
6204154 AATTTAATACTAAT
1 TATTTAATATTAAT
6204168 TATTTAAGT-TTAAT
1 TATTTAA-TATTAAT
*
6204182 GATTTAA-ATTTAAT
1 TATTTAATA-TTAAT
*
6204196 GATATAAAATAATTACTTAAT
1 --TAT---TTAA-TA-TTAAT
*
6204217 GATTTAACT-TTAAT
1 TATTTAA-TATTAAT
* *
6204231 GATTTAATAATAAT
1 TATTTAATATTAAT
* * *
6204245 TACTTAGCT-TTAAC
1 TATTTA-ATATTAAT
* * *
6204259 GATATAATAATAAT
1 TATTTAATATTAAT
*
6204273 TACTTAACT-TTAAT
1 TATTTAA-TATTAAT
* *
6204287 GATTTAATAATAAT
1 TATTTAATATTAAT
*
6204301 TATTTAATTTTAAT
1 TATTTAATATTAAT
*
6204315 GATTTAACT-TTAAT
1 TATTTAA-TATTAAT
* *
6204329 GATTTAATAATAAT
1 TATTTAATATTAAT
* *
6204343 TACTTGACT-TTAAT
1 TA-TTTAATATTAAT
6204357 TATTT-ATATT
1 TATTTAATATT
6204367 TATTGATATA
Statistics
Matches: 500, Mismatches: 114, Indels: 115
0.69 0.16 0.16
Matches are distributed among these distances:
12 1 0.00
13 14 0.03
14 406 0.81
15 45 0.09
16 9 0.02
17 1 0.00
19 6 0.01
20 3 0.01
21 8 0.02
22 7 0.01
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.49
Consensus pattern (14 bp):
TATTTAATATTAAT
Found at i:6203715 original size:28 final size:28
Alignment explanation
Indices: 6203683--6204321 Score: 372
Period size: 28 Copynumber: 22.2 Consensus size: 28
6203673 TTGAGTACAT
*
6203683 ATTTAATAATAATTATTTAAGTTTAATG
1 ATTTAATAATAATTATTTAACTTTAATG
*
6203711 ATTTAATAATAATTACTTAACTTTAATG
1 ATTTAATAATAATTATTTAACTTTAATG
* * * *
6203739 ATTTAACT-TTAATGATTTAA-TAATAATT
1 ATTTAA-TAATAATTATTTAACT-TTAATG
* * *
6203767 ACTTAACT-TTAATGATTTAACTTTAATG
1 ATTTAA-TAATAATTATTTAACTTTAATG
* *
6203795 ATTTGATAATAATTACTTAACTTTAATG
1 ATTTAATAATAATTATTTAACTTTAATG
* * * *
6203823 ATTTAA-ATCTAATGATTTAA-TAATAATT
1 ATTTAATA-ATAATTATTTAACT-TTAATG
* * *
6203851 ACTTAACT-TTAAATATTTAACTTTAATG
1 ATTTAA-TAATAATTATTTAACTTTAATG
*
6203879 ATTTAATAATAATTACTTAACTTTAATG
1 ATTTAATAATAATTATTTAACTTTAATG
* * * *
6203907 ATTTAACT-TTAATAATTTAA-TAATAATT
1 ATTTAA-TAATAATTATTTAACT-TTAATG
* * * * *
6203935 ACTTAACT-TTAATGATTTAAATTTAATA
1 ATTTAA-TAATAATTATTTAACTTTAATG
* *
6203963 ATTTAATAATATTTATTTAATTTTAATTG
1 ATTTAATAATAATTATTTAACTTTAA-TG
* *
6203992 GTTTAATAATAATTATTTAAGTTTAATG
1 ATTTAATAATAATTATTTAACTTTAATG
* * * *
6204020 ATTTAA-ATTTAATAATTTAA-TAATAATT
1 ATTTAATA-ATAATTATTTAACT-TTAATG
* * * *
6204048 ATTTAAGT-TTAATGATTTAAATTTAACG
1 ATTTAA-TAATAATTATTTAACTTTAATG
6204076 ATTTAATAATAATTATTTAATGATTTAACTTTAATG
1 ATTTAATAAT-A--A--T--T-ATTTAACTTTAATG
* *
6204112 ATTTAATAATAATTACTTAATTTTTAATG
1 ATTTAATAATAATTATTTAA-CTTTAATG
* * * *
6204141 ATTTAA-ATTTAATAATTTAA-TACTAATT
1 ATTTAATA-ATAATTATTTAACT-TTAATG
* * *
6204169 ATTTAAGT-TTAATGATTTAAATTTAATG
1 ATTTAA-TAATAATTATTTAACTTTAATG
* *
6204197 ATATAAAATAATTACTTAATGATTTAACTTTAATG
1 AT-T----TAA-TA-ATAATTATTTAACTTTAATG
* * *
6204232 ATTTAATAATAATTACTTAGCTTTAACG
1 ATTTAATAATAATTATTTAACTTTAATG
* *
6204260 ATATAATAATAATTACTTAACTTTAATG
1 ATTTAATAATAATTATTTAACTTTAATG
*
6204288 ATTTAATAATAATTATTTAATTTTAATG
1 ATTTAATAATAATTATTTAACTTTAATG
6204316 ATTTAA
1 ATTTAA
6204322 CTTTAATGAT
Statistics
Matches: 484, Mismatches: 85, Indels: 84
0.74 0.13 0.13
Matches are distributed among these distances:
27 11 0.02
28 359 0.74
29 58 0.12
30 3 0.01
31 2 0.00
33 6 0.01
34 1 0.00
35 22 0.05
36 22 0.05
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.48
Consensus pattern (28 bp):
ATTTAATAATAATTATTTAACTTTAATG
Found at i:6203756 original size:42 final size:42
Alignment explanation
Indices: 6203692--6203989 Score: 481
Period size: 42 Copynumber: 7.1 Consensus size: 42
6203682 TATTTAATAA
* *
6203692 TAATTATTTAAGTTTAATGATTTAATAATAATTACTTAACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTTAACTT
6203734 TAATGATTTAACTTTAATGATTTAATAATAATTACTTAACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTTAACTT
*
6203776 TAATGATTTAACTTTAATGATTTGATAATAATTACTTAACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTTAACTT
* *
6203818 TAATGATTTAAATCTAATGATTTAATAATAATTACTTAACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTTAACTT
6203860 TAAAT-ATTTAACTTTAATGATTTAATAATAATTACTTAACTT
1 T-AATGATTTAACTTTAATGATTTAATAATAATTACTTAACTT
*
6203902 TAATGATTTAACTTTAATAATTTAATAATAATTACTTAACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTTAACTT
* * * * *
6203944 TAATGATTTAAATTTAATAATTTAATAATATTTATTTAATTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTTAACTT
6203986 TAAT
1 TAAT
6203990 TGGTTTAATA
Statistics
Matches: 241, Mismatches: 13, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
41 3 0.01
42 235 0.98
43 3 0.01
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.49
Consensus pattern (42 bp):
TAATGATTTAACTTTAATGATTTAATAATAATTACTTAACTT
Found at i:6204168 original size:35 final size:36
Alignment explanation
Indices: 6204129--6204246 Score: 114
Period size: 35 Copynumber: 3.2 Consensus size: 36
6204119 AATAATTACT
6204129 TAATT-TTTAATGATTTAAATTTAATAATTTAATACTAA
1 TAATTATTTAATGATTTAAATTTAATAATTT-A-A-TAA
* * *
6204167 TTATTTAAGTTTAATGATTTAAATTTAATGATATAA-AA
1 -TAATT-A-TTTAATGATTTAAATTTAATAATTTAATAA
* * *
6204205 TAATTACTTAATGATTTAACTTTAATGATTTAATAA
1 TAATTATTTAATGATTTAAATTTAATAATTTAATAA
6204241 TAATTA
1 TAATTA
6204247 CTTAGCTTTA
Statistics
Matches: 68, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
35 24 0.35
36 9 0.13
37 4 0.06
38 2 0.03
39 4 0.06
40 1 0.01
41 1 0.01
42 23 0.34
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (36 bp):
TAATTATTTAATGATTTAAATTTAATAATTTAATAA
Found at i:6204335 original size:42 final size:42
Alignment explanation
Indices: 6203706--6204362 Score: 405
Period size: 42 Copynumber: 15.9 Consensus size: 42
6203696 TATTTAAGTT
* * * *
6203706 TAATGATTTAATAATAATTACTTAACTTTAATGATTTAACT-T
1 TAATTATTTAATAATAATGATTTAACTTTAATGATTTAA-TAA
* * * *
6203748 TAATGATTTAATAATAATTACTTAACTTTAATGATTTAACT-T
1 TAATTATTTAATAATAATGATTTAACTTTAATGATTTAA-TAA
* * * * *
6203790 TAATGATTTGATAATAATTACTTAACTTTAATGATTTAA-ATC
1 TAATTATTTAATAATAATGATTTAACTTTAATGATTTAATA-A
* * * *
6203832 TAATGATTTAATAATAATTACTTAACTTTAAAT-ATTTAACT-T
1 TAATTATTTAATAATAATGATTTAACTTT-AATGATTTAA-TAA
* * * *
6203874 TAATGATTTAATAATAATTACTTAACTTTAATGATTTAACT-T
1 TAATTATTTAATAATAATGATTTAACTTTAATGATTTAA-TAA
* * * *
6203916 TAATAATTTAATAATAATTACTTAACTTTAATGATTTAA-ATT
1 TAATTATTTAATAATAATGATTTAACTTTAATGATTTAATA-A
* * * * *
6203958 TAATAATTTAATAATATTTATTTAATTTTAATTGGTTTAATAA
1 TAATTATTTAATAATAATGATTTAACTTTAA-TGATTTAATAA
* * *
6204001 TAATTATTTAAGT-TTAATGATTTAAATTTAATAATTTAATAA
1 TAATTATTTAA-TAATAATGATTTAACTTTAATGATTTAATAA
* * *
6204043 TAATTATTTAAGT-TTAATGATTTAAATTTAACGATTTAATAA
1 TAATTATTTAA-TAATAATGATTTAACTTTAATGATTTAATAA
6204085 TAATTA--T--T--TAATGATTTAACTTTAATGATTTAATAA
1 TAATTATTTAATAATAATGATTTAACTTTAATGATTTAATAA
* ** * * *
6204121 TAATTACTTAATTTTTAATGATTTAAATTTAATAATTTAATAC
1 TAATTATTTAA-TAATAATGATTTAACTTTAATGATTTAATAA
* *
6204164 TAATTATTTAAGT-TTAATGATTTAAATTTAATGA--T-ATAA
1 TAATTATTTAA-TAATAATGATTTAACTTTAATGATTTAATAA
* *
6204203 -AA-TAATTACT--TAATGATTTAACTTTAATGATTTAATAA
1 TAATTATTTAATAATAATGATTTAACTTTAATGATTTAATAA
* * * * * * * * *
6204241 TAATTACTTAGCT-TTAACGATATAA-TAATAATTACTTAACT-T
1 TAATTATTTA-ATAATAATGATTTAACT-TTAATGATTTAA-TAA
* * * *
6204283 TAATGATTTAATAATAATTATTTAATTTTAATGATTTAACT-T
1 TAATTATTTAATAATAATGATTTAACTTTAATGATTTAA-TAA
* * * * *
6204325 TAATGATTTAATAATAATTACTTGACTTTAATTATTTA
1 TAATTATTTAATAATAATGATTTAACTTTAATGATTTA
6204363 TATTTATTGA
Statistics
Matches: 534, Mismatches: 52, Indels: 58
0.83 0.08 0.09
Matches are distributed among these distances:
35 19 0.04
36 33 0.06
37 7 0.01
38 7 0.01
39 5 0.01
40 7 0.01
41 8 0.01
42 374 0.70
43 72 0.13
44 2 0.00
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (42 bp):
TAATTATTTAATAATAATGATTTAACTTTAATGATTTAATAA
Found at i:6207164 original size:2 final size:2
Alignment explanation
Indices: 6207157--6207218 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
6207147 CTAACAGTTG
6207157 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6207199 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
6207219 TTAAAAAAAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6214256 original size:30 final size:31
Alignment explanation
Indices: 6214221--6214310 Score: 107
Period size: 30 Copynumber: 2.9 Consensus size: 31
6214211 GAAGGACCTA
6214221 TCCATATGTTCCGAAGAACATAGGTAACT-T
1 TCCATATGTTCCGAAGAACATAGGTAACTAT
* *
6214251 TCCATATGTCCCGAAGGACATAGGTAAACTAT
1 TCCATATGTTCCGAAGAACATAGGT-AACTAT
6214283 T-CATATG-TCTCGAA-AGACATAGGTAACT
1 TCCATATGTTC-CGAAGA-ACATAGGTAACT
6214311 CTCGACTCTT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
30 28 0.54
31 22 0.42
32 2 0.04
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (31 bp):
TCCATATGTTCCGAAGAACATAGGTAACTAT
Found at i:6214291 original size:31 final size:31
Alignment explanation
Indices: 6214218--6214308 Score: 114
Period size: 31 Copynumber: 3.0 Consensus size: 31
6214208 CTCGAAGGAC
* * *
6214218 CTATCCATATGTTCCGAAGAACATAGGT-AA
1 CTATTCATATGTCCCGAAGGACATAGGTAAA
6214248 CT-TTCCATATGTCCCGAAGGACATAGGTAAA
1 CTATT-CATATGTCCCGAAGGACATAGGTAAA
* *
6214279 CTATTCATATGTCTCGAAAGACATAGGTAA
1 CTATTCATATGTCCCGAAGGACATAGGTAA
6214309 CTCTCGACTC
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
29 1 0.02
30 23 0.43
31 27 0.51
32 2 0.04
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (31 bp):
CTATTCATATGTCCCGAAGGACATAGGTAAA
Found at i:6214503 original size:2 final size:2
Alignment explanation
Indices: 6214492--6214538 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
6214482 TTTATATTTC
6214492 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6214533 AT AT AT
1 AT AT AT
6214539 TGTCCTATTC
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:6214706 original size:2 final size:2
Alignment explanation
Indices: 6214699--6214746 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
6214689 TTATTATTTC
6214699 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6214741 AT AT AT
1 AT AT AT
6214747 TCATGTCCTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6217137 original size:18 final size:18
Alignment explanation
Indices: 6217114--6217148 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
6217104 AAGTTAGCAT
6217114 TTTGCATAAA-CCTTATTA
1 TTTGCA-AAATCCTTATTA
6217132 TTTGCAAAATCCTTATT
1 TTTGCAAAATCCTTATT
6217149 CAAATTACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.46
Consensus pattern (18 bp):
TTTGCAAAATCCTTATTA
Found at i:6219876 original size:18 final size:18
Alignment explanation
Indices: 6219826--6219885 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
6219816 CAATAATATC
*
6219826 ATCATAATCTCTATCATT
1 ATCATGATCTCTATCATT
* **
6219844 ATCCA-CATCAATATCATT
1 AT-CATGATCTCTATCATT
*
6219862 ATCATGATCTCTATCACT
1 ATCATGATCTCTATCATT
6219880 ATCATG
1 ATCATG
6219886 TATTAACTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
17 2 0.06
18 29 0.88
19 2 0.06
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.38
Consensus pattern (18 bp):
ATCATGATCTCTATCATT
Found at i:6220222 original size:76 final size:76
Alignment explanation
Indices: 6220096--6220248 Score: 306
Period size: 76 Copynumber: 2.0 Consensus size: 76
6220086 TGCTGTCACC
6220096 ACAGCTCGTATAAATGTTTCGAAGGACCTATCCAGAGGTCATAAAGAACCTCGACAACTATCCAT
1 ACAGCTCGTATAAATGTTTCGAAGGACCTATCCAGAGGTCATAAAGAACCTCGACAACTATCCAT
6220161 AGGTCCTGAAG
66 AGGTCCTGAAG
6220172 ACAGCTCGTATAAATGTTTCGAAGGACCTATCCAGAGGTCATAAAGAACCTCGACAACTATCCAT
1 ACAGCTCGTATAAATGTTTCGAAGGACCTATCCAGAGGTCATAAAGAACCTCGACAACTATCCAT
6220237 AGGTCCTGAAG
66 AGGTCCTGAAG
6220248 A
1 A
6220249 ACCTAGGTAA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.22
Consensus pattern (76 bp):
ACAGCTCGTATAAATGTTTCGAAGGACCTATCCAGAGGTCATAAAGAACCTCGACAACTATCCAT
AGGTCCTGAAG
Found at i:6220279 original size:31 final size:31
Alignment explanation
Indices: 6220227--6220289 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
6220217 GAACCTCGAC
* *
6220227 AACTATCCATAGGTCCTGAAGAACCTAGGTA
1 AACTATCCATAGGTCCCGAAGAACATAGGTA
* *
6220258 AACTGTCCATATGTCCCGAAGAACATAGGTA
1 AACTATCCATAGGTCCCGAAGAACATAGGTA
6220289 A
1 A
6220290 CCCTCGACTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (31 bp):
AACTATCCATAGGTCCCGAAGAACATAGGTA
Found at i:6222694 original size:30 final size:30
Alignment explanation
Indices: 6222656--6222747 Score: 123
Period size: 30 Copynumber: 3.0 Consensus size: 30
6222646 CCCAAAGGAC
*
6222656 CTATCCATATGTTTCGAAGAACATAGGTAA
1 CTATCCATATGTCTCGAAGAACATAGGTAA
* * *
6222686 CTGTCCATATGTCCCGAAGGACATAGGTAAA
1 CTATCCATATGTCTCGAAGAACATAGGT-AA
6222717 CTATCCATATGTCTCGAA-AGACATAGGTAA
1 CTATCCATATGTCTCGAAGA-ACATAGGTAA
6222747 C
1 C
6222748 CCTCGACTCT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
30 27 0.51
31 26 0.49
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (30 bp):
CTATCCATATGTCTCGAAGAACATAGGTAA
Found at i:6222727 original size:31 final size:31
Alignment explanation
Indices: 6222656--6222746 Score: 130
Period size: 31 Copynumber: 3.0 Consensus size: 31
6222646 CCCAAAGGAC
* *
6222656 CTATCCATATGTTTCGAAGAACATAGGT-AA
1 CTATCCATATGTCTCGAAGGACATAGGTAAA
* *
6222686 CTGTCCATATGTCCCGAAGGACATAGGTAAA
1 CTATCCATATGTCTCGAAGGACATAGGTAAA
*
6222717 CTATCCATATGTCTCGAAAGACATAGGTAA
1 CTATCCATATGTCTCGAAGGACATAGGTAA
6222747 CCCTCGACTC
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 24 0.45
31 29 0.55
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (31 bp):
CTATCCATATGTCTCGAAGGACATAGGTAAA
Found at i:6223540 original size:22 final size:22
Alignment explanation
Indices: 6223512--6223554 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
6223502 ACTATACGGC
*
6223512 ATGAACAATGCCATGAACAGTA
1 ATGAACAATACCATGAACAGTA
6223534 ATGAACAATACCATGAACAGT
1 ATGAACAATACCATGAACAGT
6223555 GAAATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.47, C:0.19, G:0.16, T:0.19
Consensus pattern (22 bp):
ATGAACAATACCATGAACAGTA
Found at i:6241456 original size:20 final size:20
Alignment explanation
Indices: 6241431--6241475 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
6241421 TCGAAGATGA
6241431 TAAGTCCTTCGGA-CCATCAG
1 TAAGT-CTTCGGAGCCATCAG
**
6241451 TAAGTCTTTTGAGCCATCAG
1 TAAGTCTTCGGAGCCATCAG
6241471 TAAGT
1 TAAGT
6241476 TTTTCGTGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (20 bp):
TAAGTCTTCGGAGCCATCAG
Found at i:6241797 original size:42 final size:42
Alignment explanation
Indices: 6241692--6241812 Score: 125
Period size: 42 Copynumber: 2.9 Consensus size: 42
6241682 TTTAGTAAGA
* * *
6241692 CCTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGATTAAAT
1 CCTTCAGGTCATCTGTAAGTCTTTTGAGCATGATGATTAAAT
* * *
6241734 CCTTCATGTCATTTGTAAGTCTTTTGAGTATGATGATTAAAT
1 CCTTCAGGTCATCTGTAAGTCTTTTGAGCATGATGATTAAAT
** * * * * *
6241776 TTTTCGGGTTATCTGTCAGTCTTTCGAGCAAGATGAT
1 CCTTCAGGTCATCTGTAAGTCTTTTGAGCATGATGAT
6241813 AAGTTCTCTG
Statistics
Matches: 63, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.40
Consensus pattern (42 bp):
CCTTCAGGTCATCTGTAAGTCTTTTGAGCATGATGATTAAAT
Found at i:6241886 original size:37 final size:37
Alignment explanation
Indices: 6241836--6241972 Score: 220
Period size: 37 Copynumber: 3.7 Consensus size: 37
6241826 TATCTTAACA
* * *
6241836 CTTCACGGAAGAGTAGTGAAGTAAATCAATCTCAAGC
1 CTTCACGGAAGAGTAGTGAAGCAAATCAATTTTAAGC
* *
6241873 CTTCACAGAAGAGTAGTGAAGCAAATTAATTTTAAGC
1 CTTCACGGAAGAGTAGTGAAGCAAATCAATTTTAAGC
*
6241910 CTTCATGGAAGAGTAGTGAAGCAAATCAATTTTAAGC
1 CTTCACGGAAGAGTAGTGAAGCAAATCAATTTTAAGC
6241947 CTTCACGGAAGAGTAGTGAAGCAAAT
1 CTTCACGGAAGAGTAGTGAAGCAAAT
6241973 TAAGATCTTA
Statistics
Matches: 91, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 91 1.00
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (37 bp):
CTTCACGGAAGAGTAGTGAAGCAAATCAATTTTAAGC
Found at i:6254888 original size:20 final size:20
Alignment explanation
Indices: 6254863--6254900 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
6254853 CGCCAAACAC
6254863 TCTTCTTTGTCTCATTCTTT
1 TCTTCTTTGTCTCATTCTTT
*
6254883 TCTTCTTTTTCTCATTCT
1 TCTTCTTTGTCTCATTCT
6254901 CCTTCTCCAA
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:0.05, C:0.26, G:0.03, T:0.66
Consensus pattern (20 bp):
TCTTCTTTGTCTCATTCTTT
Found at i:6260413 original size:40 final size:40
Alignment explanation
Indices: 6260328--6260420 Score: 143
Period size: 40 Copynumber: 2.3 Consensus size: 40
6260318 ATTTTCCGAT
6260328 TATCGCAATGCGAATATGTAAATCGCAATGCGAATATGTA
1 TATCGCAATGCGAATATGTAAATCGCAATGCGAATATGTA
* *
6260368 AATCGCAATGCGAATATGTAAATCGCAATGCGATTATG-A
1 TATCGCAATGCGAATATGTAAATCGCAATGCGAATATGTA
*
6260407 CTATCGCAACGCGA
1 -TATCGCAATGCGA
6260421 TTCTGACTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
39 1 0.02
40 47 0.98
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (40 bp):
TATCGCAATGCGAATATGTAAATCGCAATGCGAATATGTA
Found at i:6260415 original size:20 final size:20
Alignment explanation
Indices: 6260329--6260405 Score: 145
Period size: 20 Copynumber: 3.9 Consensus size: 20
6260319 TTTTCCGATT
6260329 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
6260349 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
6260369 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
6260389 ATCGCAATGCGATTATG
1 ATCGCAATGCGAATATG
6260406 ACTATCGCAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:6260420 original size:20 final size:20
Alignment explanation
Indices: 6260389--6260436 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
6260379 GAATATGTAA
*
6260389 ATCGCAATGCGATTATGACT
1 ATCGCAACGCGATTATGACT
*
6260409 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTATGACT
*
6260429 GTCGCAAC
1 ATCGCAAC
6260437 ACTGAATTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTATGACT
Found at i:6261219 original size:24 final size:24
Alignment explanation
Indices: 6261187--6261240 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
6261177 GTATTCGAAA
*
6261187 TTTGATCTTGGTTAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
6261211 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
6261235 TTTGAT
1 TTTGAT
6261241 GATGTTTTAG
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:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:6261447 original size:14 final size:14
Alignment explanation
Indices: 6261418--6261454 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
6261408 TAACCCTGAA
6261418 GAAGAACAAATCCCC
1 GAAGAA-AAATCCCC
*
6261433 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
6261447 GAAGAAAA
1 GAAGAAAA
6261455 TGCCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.24, G:0.19, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:6263837 original size:140 final size:140
Alignment explanation
Indices: 6263585--6263854 Score: 504
Period size: 140 Copynumber: 1.9 Consensus size: 140
6263575 AAACGTTGTA
6263585 TTATGTGTAAACTTTTAACAATTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACAATTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
* *
6263650 TGATCTGTTTAGTTATTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTATTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
6263715 TATGTGTATT
131 TATGTGTATT
*
6263725 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACAATTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
*
6263790 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTATTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
6263855 CGCAACTCAA
Statistics
Matches: 126, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 126 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACAATTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTATTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:6263850 original size:20 final size:20
Alignment explanation
Indices: 6263825--6264049 Score: 222
Period size: 20 Copynumber: 11.8 Consensus size: 20
6263815 TTACACATTC
*
6263825 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
6263845 ATTTGACTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
* *
6263864 A----A-AATCACAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
6263879 ATTTGACTATCGTAACACGA
1 ATTTGACTATCGCAACGCGA
*
6263899 ATATGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
* *
6263918 A----A-AATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
* *
6263933 ATTTGTCTATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
6263953 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
6263973 ATTTGACTATCGCAACGCAA
1 ATTTGACTATCGCAACGCGA
*
6263993 ATTTGAGTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
6264013 ATTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
6264033 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
6264050 AGAAAATCGC
Statistics
Matches: 168, Mismatches: 25, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
14 17 0.10
15 6 0.04
19 5 0.03
20 140 0.83
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:6263907 original size:54 final size:54
Alignment explanation
Indices: 6263825--6264029 Score: 230
Period size: 54 Copynumber: 3.7 Consensus size: 54
6263815 TTACACATTC
* *
6263825 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACTCAAAAATCACAACGCGA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAAAATCACAACGCGA
* * * * *
6263879 ATTTGACTATCGTAACACGAATATGACTATCGCAACGCAAAAATCGCAATGCGA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAAAATCACAACGCGA
* * * * *
6263933 ATTTGTCTATCGCAATGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGC-AA----A-AATCACAACGCGA
* *
6263993 ATTTGAGTATCGCAACGCGAATTTGATTATCGCAACG
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACG
6264030 GGTATTTGAC
Statistics
Matches: 126, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
54 80 0.63
55 2 0.02
59 1 0.01
60 43 0.34
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (54 bp):
ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAAAATCACAACGCGA
Found at i:6264117 original size:20 final size:20
Alignment explanation
Indices: 6264092--6264130 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6264082 CGTAAATTGA
*
6264092 CTTTCGCGTTGCGATTTTGT
1 CTTTCGCATTGCGATTTTGT
*
6264112 CTTTCGTATTGCGATTTTG
1 CTTTCGCATTGCGATTTTG
6264131 AGTTTAGCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.18, G:0.23, T:0.51
Consensus pattern (20 bp):
CTTTCGCATTGCGATTTTGT
Done.