Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008531.1 Hibiscus syriacus cultivar Beakdansim tig00111409_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: 3817888
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 19
Found at i:2621351 original size:3 final size:3
Alignment explanation
Indices: 2621308--2621449 Score: 121
Period size: 3 Copynumber: 46.7 Consensus size: 3
2621298 ACATATTCTT
* * * *
2621308 TTA TTA TTT TTA CTA CTA TTAA TTA TTT TTA TTA GTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA -TTA TTA TTA TTA
* * * *
2621355 TTA TTA TTA TTTA TCTA TTA TTA TTG TTG TTG TTA TTA TCT- TTA TTT
1 TTA TTA TTA -TTA T-TA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
*
2621402 TTA TTA GTA TT- TTA -TA TTA TTA -TA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
2621445 TTA TT
1 TTA TT
2621450 TCATATATAT
Statistics
Matches: 117, Mismatches: 12, Indels: 20
0.79 0.08 0.13
Matches are distributed among these distances:
2 7 0.06
3 95 0.81
4 15 0.13
ACGTcount: A:0.27, C:0.03, G:0.04, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2622844 original size:102 final size:103
Alignment explanation
Indices: 2622707--2622984 Score: 459
Period size: 103 Copynumber: 2.7 Consensus size: 103
2622697 ATATTAAACC
* * * *
2622707 TTAATATGACCTTGTGGTGACCCGTCTTGGGGTATGATCAACATTATTTATGGTACATGTAAAAT
1 TTAATACGACCTTGTGGTGACCCGCCCTGGGGTATGATCAACATTATTTATGGTCCATGTAAAAT
*
2622772 TCTAATTTCTAACCGCTAA-TTTTTTATTGTTCGAATG
66 TCTAATTTCTAACCACTAACTTTTTTATTGTTCGAATG
* *
2622809 TTAATACGACCTTGTGGTGACCTGCCCTGGGGTATGATCAACATTATTTATGGTCCAGGTAAAAT
1 TTAATACGACCTTGTGGTGACCCGCCCTGGGGTATGATCAACATTATTTATGGTCCATGTAAAAT
2622874 TCTAATTTCTAACCACTAACTTTTTTATTGTTCGAATG
66 TCTAATTTCTAACCACTAACTTTTTTATTGTTCGAATG
* * *
2622912 TTAATACGACCTTGTGGTGACCCGCCCTGGGGTATGATCCATATTATTCATGGTCCATGTAAAAT
1 TTAATACGACCTTGTGGTGACCCGCCCTGGGGTATGATCAACATTATTTATGGTCCATGTAAAAT
2622977 TCTAATTT
66 TCTAATTT
2622985 TTTATTTTCC
Statistics
Matches: 163, Mismatches: 12, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
102 77 0.47
103 86 0.53
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (103 bp):
TTAATACGACCTTGTGGTGACCCGCCCTGGGGTATGATCAACATTATTTATGGTCCATGTAAAAT
TCTAATTTCTAACCACTAACTTTTTTATTGTTCGAATG
Found at i:2625447 original size:23 final size:22
Alignment explanation
Indices: 2625420--2625470 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 22
2625410 AAGATTAATA
2625420 AAAATATTAATATATTTA-ATGTG
1 AAAA-ATTAATATATTTAGATG-G
2625443 -AAAATTAATATATTTAGATGG
1 AAAAATTAATATATTTAGATGG
2625464 AAAAATT
1 AAAAATT
2625471 TTAAAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (22 bp):
AAAAATTAATATATTTAGATGG
Found at i:2625509 original size:26 final size:26
Alignment explanation
Indices: 2625473--2625523 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
2625463 GAAAAATTTT
2625473 AAAAAAATATTATATA-AATTTTTGA
1 AAAAAAATATTATATACAATTTTTGA
*
2625498 AAAAATAATATTTTATACAATTTTTG
1 AAAAA-AATATTATATACAATTTTTG
2625524 TCTATCATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.22
26 10 0.43
27 8 0.35
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (26 bp):
AAAAAAATATTATATACAATTTTTGA
Found at i:2630162 original size:155 final size:155
Alignment explanation
Indices: 2629900--2630189 Score: 424
Period size: 155 Copynumber: 1.9 Consensus size: 155
2629890 TAATGGTTTT
* * *
2629900 TTAATCCATACATTATTTTAAATAATTGTTACCTTAATTCACAAGACGGAAATATTATGCATTAA
1 TTAATCCAAACATTATTTTAAATAATTGCTACCTTAATTCACAAGACAGAAATATTATGCATTAA
*
2629965 TGTTTCCTTAAATATCAAACGAGAATATTAGGAATTAATGGCTCCTTGATTC-GCAAAATTAAAT
66 TGTTTCCTTAAATATCAAACGAGAATATTAGGAATTAATGGCTCATTGATTCTG-AAAATTAAAT
2630029 TAAATTAAATTGGATTTAATGACTCC
130 TAAATTAAATTGGATTTAATGACTCC
* **
2630055 TTAATTCAAACATTATTTTAGGTAATTGCTACCTTAATTCACAAGACA-AGAATATTATGCATTA
1 TTAATCCAAACATTATTTTAAATAATTGCTACCTTAATTCACAAGACAGA-AATATTATGCATTA
* * * * *
2630119 ATGTTTCCTTGATTATCGAACGAGAATATTA-TACATTAATGGCTCATTGATTCTGGAAATTAAA
65 ATGTTTCCTTAAATATCAAACGAGAATATTAGGA-ATTAATGGCTCATTGATTCTGAAAATTAAA
2630183 TTAAATT
129 TTAAATT
2630190 TGATTTAATG
Statistics
Matches: 120, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
154 2 0.02
155 117 0.98
156 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (155 bp):
TTAATCCAAACATTATTTTAAATAATTGCTACCTTAATTCACAAGACAGAAATATTATGCATTAA
TGTTTCCTTAAATATCAAACGAGAATATTAGGAATTAATGGCTCATTGATTCTGAAAATTAAATT
AAATTAAATTGGATTTAATGACTCC
Found at i:2630996 original size:17 final size:17
Alignment explanation
Indices: 2630974--2631017 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
2630964 ATTTTATGGT
2630974 TTAAGGGGATATGATGC
1 TTAAGGGGATATGATGC
2630991 TTAAGGGGATATGATGC
1 TTAAGGGGATATGATGC
2631008 TTAAGGGGAT
1 TTAAGGGGAT
2631018 GACGCACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.30, C:0.05, G:0.36, T:0.30
Consensus pattern (17 bp):
TTAAGGGGATATGATGC
Found at i:2635452 original size:21 final size:21
Alignment explanation
Indices: 2635426--2635484 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
2635416 TAGTAAAGCA
*
2635426 TTATCGGTTTTGTTATTTTTT
1 TTATCGATTTTGTTATTTTTT
*
2635447 TTATCGATTTTATTATTTTTT
1 TTATCGATTTTGTTATTTTTT
* *
2635468 CTATTGATTTTGTTATT
1 TTATCGATTTTGTTATT
2635485 GTTTAGCACT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.15, C:0.05, G:0.10, T:0.69
Consensus pattern (21 bp):
TTATCGATTTTGTTATTTTTT
Found at i:2636720 original size:2 final size:2
Alignment explanation
Indices: 2636713--2636744 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2636703 ATTATATGTG
2636713 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
2636745 TTACTACAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2637777 original size:18 final size:18
Alignment explanation
Indices: 2637708--2637777 Score: 59
Period size: 18 Copynumber: 3.7 Consensus size: 18
2637698 ATATCTCTCT
2637708 ATATATTATTTTTAATTA
1 ATATATTATTTTTAATTA
* * *
2637726 AGTCTATGTTTTTATTGAATAA
1 A-TATAT-TATTT-TT-AATTA
* *
2637748 AAATAATATTTTTAATTA
1 ATATATTATTTTTAATTA
2637766 ATATATTATTTT
1 ATATATTATTTT
2637778 GGTTCGGGTC
Statistics
Matches: 38, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
18 15 0.39
19 6 0.16
20 8 0.21
21 4 0.11
22 5 0.13
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (18 bp):
ATATATTATTTTTAATTA
Found at i:2641597 original size:29 final size:29
Alignment explanation
Indices: 2641555--2641613 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
2641545 GCTCCCCAGA
2641555 AGGAGATACTTGGACAAATGAACCTTCAG
1 AGGAGATACTTGGACAAATGAACCTTCAG
* *
2641584 AGGAGATATTTGGACAAATGAACTTTCAG
1 AGGAGATACTTGGACAAATGAACCTTCAG
2641613 A
1 A
2641614 CAACTTGAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.24
Consensus pattern (29 bp):
AGGAGATACTTGGACAAATGAACCTTCAG
Found at i:2645396 original size:161 final size:160
Alignment explanation
Indices: 2645228--2645726 Score: 700
Period size: 161 Copynumber: 3.1 Consensus size: 160
2645218 ATCTAACTTT
*
2645228 TTATGTGATGAATGAGCCAAGGTCGGTGTTGTTCCAACTCCTTATATGATGGAATCAATG-AAAT
1 TTATGTGATGAATGAGCCAAGGTGGGTGTTGTTCCAACTCCTTATATGATGGAATCAA-GAAAAT
* *
2645292 GTTGAACAAGTTCTTCTTATTACAAACTTCTCCTATTGGGAATATCGATCCAACTCTTTCTGCGA
65 GTTGAACAAGTTCTTCTTATTACAAACTTCTCCTATTGGGAATGTCGATCCAACTCCTTCTGCGA
* *
2645357 TGGATGATTCAAGGTGATGCTGATCCAACTCC
130 TGGATGA-CCAAGGTGACGCTGATCCAACTCC
* * * *
2645389 TTATGTGATGGATGAACCAAGGTGGGTGTTGTTCCATA-TCCTTATGTGATGGAATCAAGCAAAT
1 TTATGTGATGAATGAGCCAAGGTGGGTGTTGTTCCA-ACTCCTTATATGATGGAATCAAGAAAAT
* * *
2645453 GTTGAGA-AAGTTCTTCTTATTACTAACTTCTCCTATTGGGAATGTCGATACAACTCCTTCTGCA
65 GTTGA-ACAAGTTCTTCTTATTACAAACTTCTCCTATTGGGAATGTCGATCCAACTCCTTCTGCG
*
2645517 ATGGATGACCCAAGGTGACGCTAATCCAACTCC
129 ATGGATGA-CCAAGGTGACGCTGATCCAACTCC
2645550 TTATGTGAT-AGATGAGCCAAGGTGGGTGTTGTTCCAACTCCTTATATGATGGAATCAAGAAAAT
1 TTATGTGATGA-ATGAGCCAAGGTGGGTGTTGTTCCAACTCCTTATATGATGGAATCAAGAAAAT
* * ** * *
2645614 GTTGAGCAAGTTCTTCTTATTACAAACTTCTCCTATCGATAATGTTGATCTAACTCCTTCTGCGA
65 GTTGAACAAGTTCTTCTTATTACAAACTTCTCCTATTGGGAATGTCGATCCAACTCCTTCTGCGA
* **
2645679 TGGATGACCTAAGGTGACACTGATCCAACTTA
130 TGGATGACC-AAGGTGACGCTGATCCAACTCC
*
2645711 TTATGTGATGGATGAG
1 TTATGTGATGAATGAG
2645727 ATTAAGTTCT
Statistics
Matches: 299, Mismatches: 31, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
160 4 0.01
161 293 0.98
162 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33
Consensus pattern (160 bp):
TTATGTGATGAATGAGCCAAGGTGGGTGTTGTTCCAACTCCTTATATGATGGAATCAAGAAAATG
TTGAACAAGTTCTTCTTATTACAAACTTCTCCTATTGGGAATGTCGATCCAACTCCTTCTGCGAT
GGATGACCAAGGTGACGCTGATCCAACTCC
Found at i:2645399 original size:40 final size:41
Alignment explanation
Indices: 2645338--2645441 Score: 113
Period size: 40 Copynumber: 2.6 Consensus size: 41
2645328 TGGGAATATC
* * * **
2645338 GATCCAACTCTTTCTGCGATGGATGATTCAAGGT-GATGCT
1 GATCCAACTCCTTATGTGATGGATGAACCAAGGTGGATGCT
* *
2645378 GATCCAACTCCTTATGTGATGGATGAACCAAGGTGGGTGTT
1 GATCCAACTCCTTATGTGATGGATGAACCAAGGTGGATGCT
*
2645419 GTTCCATA-TCCTTATGTGATGGA
1 GATCCA-ACTCCTTATGTGATGGA
2645442 ATCAAGCAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
40 29 0.54
41 24 0.44
42 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (41 bp):
GATCCAACTCCTTATGTGATGGATGAACCAAGGTGGATGCT
Found at i:2650145 original size:14 final size:14
Alignment explanation
Indices: 2650126--2650152 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2650116 GAATGTAAAA
2650126 AATAAAGAATATGG
1 AATAAAGAATATGG
2650140 AATAAAGAATATG
1 AATAAAGAATATG
2650153 ATGCAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.19, T:0.22
Consensus pattern (14 bp):
AATAAAGAATATGG
Found at i:2654970 original size:81 final size:81
Alignment explanation
Indices: 2654832--2655553 Score: 1032
Period size: 81 Copynumber: 8.9 Consensus size: 81
2654822 CGTCTAGAGC
* * * * ** *
2654832 ATTTAACCTTTCATCTAACTGGCATGAA-TGATACATTTCTGCCAAATGCACAGCTAGGCTTTTG
1 ATTTAACCTTTCATCTAACTGGCAT-AATTGACACCTTTCTGTCAAATGCACAACTAGGCCATTA
* *
2654896 GTCTTTTACTCAAAGGC
65 ATCTTTTACTCAAAGGT
* * * * * *
2654913 ATTTAACCTTTTATCTAACTGGCATGATTGACACATTTCTGCCAAATGCACAACTAGGCTAATAA
1 ATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCATTAA
*
2654978 TCTTTTACACAAAGGT
66 TCTTTTACTCAAAGGT
* * * *
2654994 ATTTAGCCTTTCATCTAACAGGCATATTTGATACCTTTCTGTCAAATGCACAACTAGGCCATTAA
1 ATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCATTAA
* *
2655059 TCATTTACACAAAGGT
66 TCTTTTACTCAAAGGT
*
2655075 ATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATACACAACTAGGCCATTAA
1 ATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCATTAA
2655140 TCTTTTACTCAAAGGT
66 TCTTTTACTCAAAGGT
* * * *
2655156 ATTTAACCTTTCATCTAACTGGTATAATTGACACCTTTTTGTCAAAAGAACAACTAGGCCATTAA
1 ATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCATTAA
*
2655221 TCTTTTACTCAAAGAT
66 TCTTTTACTCAAAGGT
* ** *
2655237 ATTTAACCATAAATCTAATTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCATTAA
1 ATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCATTAA
2655302 TCTTTTACTCAAAGGT
66 TCTTTTACTCAAAGGT
* * *
2655318 ATGTAACCTTTTATCTAATTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCATTAA
1 ATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCATTAA
2655383 TCTTTTACTCAAAGGT
66 TCTTTTACTCAAAGGT
* * *
2655399 ATTTAACCTTTCATATAACTCGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCCATTAA
1 ATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCATTAA
*
2655464 TCTTTTTCTCAAAGGT
66 TCTTTTACTCAAAGGT
* * * * *
2655480 TTTTAACCTTTCATCTAACTGGAATAATTGTCACCGTTCTGTCAAATGCACAGCTAGGCCATTAA
1 ATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCATTAA
2655545 TCTTTTACT
66 TCTTTTACT
2655554 TTAGAACAGT
Statistics
Matches: 579, Mismatches: 61, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
80 1 0.00
81 578 1.00
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (81 bp):
ATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCATTAA
TCTTTTACTCAAAGGT
Found at i:2660072 original size:66 final size:66
Alignment explanation
Indices: 2659966--2660094 Score: 258
Period size: 66 Copynumber: 2.0 Consensus size: 66
2659956 ATAAATGTAA
2659966 CACCCATTTCCAGTATACATTTCCATACACAAGTAATACGTGTCACATGATTTTTTTAAAAACGT
1 CACCCATTTCCAGTATACATTTCCATACACAAGTAATACGTGTCACATGATTTTTTTAAAAACGT
2660031 T
66 T
2660032 CACCCATTTCCAGTATACATTTCCATACACAAGTAATACGTGTCACATGATTTTTTTAAAAAC
1 CACCCATTTCCAGTATACATTTCCATACACAAGTAATACGTGTCACATGATTTTTTTAAAAAC
2660095 CAAAACCTTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (66 bp):
CACCCATTTCCAGTATACATTTCCATACACAAGTAATACGTGTCACATGATTTTTTTAAAAACGT
T
Found at i:2660837 original size:81 final size:81
Alignment explanation
Indices: 2660747--2661541 Score: 1042
Period size: 81 Copynumber: 9.8 Consensus size: 81
2660737 TCATTTAAAT
* * ** *
2660747 TTTCATCTAACTAGCATGATTGACACCTTTCTG-CTAAATGCACAACTAGGCTTTTAGTCTTTTA
1 TTTCATCTAACTGGCATAATTGACACCTTTCTGTC-AAATGCACAACTAGGCCATTAATCTTTTA
* *
2660811 CTCAAAGGCATTTAATC
65 CTCAAAGGTATTTAACC
* *
2660828 TTTCATCTAACAT-GCATGATTGACACCTTTCTGCCAAATGCACAACTAGGCCATTAATCTTTTA
1 TTTCATCTAAC-TGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCATTAATCTTTTA
* *
2660892 CTCAAATGTATTTAATC
65 CTCAAAGGTATTTAACC
* * * *
2660909 TTTTATCTAACTGGCATAATTGACACATTTCTGTCAAATGAAAAACTAGGCCATTAATCTTTTAC
1 TTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCATTAATCTTTTAC
2660974 TCAAAGGTATTTAACC
66 TCAAAGGTATTTAACC
* *
2660990 TTTCGTCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCATTAATCTTTTCC
1 TTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCATTAATCTTTTAC
2661055 TCAAAGGTATTTAACC
66 TCAAAGGTATTTAACC
* * *
2661071 TTTCATCTAACTGGCATAGTTGACACCTTTCTGTCAAATTCACAACTAGGCCATTAATATTTTAC
1 TTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCATTAATCTTTTAC
* *
2661136 TC-AAGCATATTTAAAC
66 TCAAAG-GTATTTAACC
* * * ** * *
2661152 TTTCATCTAACTGGCATAATTGACACATTTATGTCAAATGAACGTCAAGGCTATTAATCTTTTAC
1 TTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCATTAATCTTTTAC
* *
2661217 TC-AAGCATATTTAAAC
66 TCAAAG-GTATTTAACC
* * * *
2661233 TTTCATCTAACTCGCATAATTGACACCTTTCTAT-ATAATGGACAATTAGGCCATTAATCTTTTA
1 TTTCATCTAACTGGCATAATTGACACCTTTCTGTCA-AATGCACAACTAGGCCATTAATCTTTTA
2661297 CTCAAAGGTATTTAACC
65 CTCAAAGGTATTTAACC
* * ** *
2661314 TTTCATCTAACTAGCATAATTGGCATATTTCTGTCAAATGCACAGCTAGGCCATTAATCTTTTAC
1 TTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCATTAATCTTTTAC
2661379 TCAAAGGTATTTAACC
66 TCAAAGGTATTTAACC
* * * * * *
2661395 TTTCATCTAACTGGCCTAATTGACACATTTCTTTCAAATGCACAGCTAGGTCATTAATATTTTAC
1 TTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCATTAATCTTTTAC
2661460 TCAAAGGTATTTAACC
66 TCAAAGGTATTTAACC
** * * * *
2661476 TTTCATCTAAAAGACATAATTGACATCTTTCTGTCAAATGCACAACTAGACCATTAATATTTTAC
1 TTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCATTAATCTTTTAC
2661541 T
66 T
2661542 TTAGAACAGT
Statistics
Matches: 634, Mismatches: 73, Indels: 14
0.88 0.10 0.02
Matches are distributed among these distances:
80 5 0.01
81 623 0.98
82 6 0.01
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (81 bp):
TTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCATTAATCTTTTAC
TCAAAGGTATTTAACC
Found at i:2669939 original size:52 final size:52
Alignment explanation
Indices: 2669788--2670107 Score: 406
Period size: 52 Copynumber: 6.0 Consensus size: 52
2669778 TCAGTTAACT
* *
2669788 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATAAAAG
1 GCCTAACTGTGCAT-TTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAG
*
2669841 GCCTAACTATGCATATTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAG
1 GCCTAACTGTGCAT-TTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAG
**
2669894 GCCTAACTGTGCATTTGATAGAAAGGTGCCAATAATGCAAGTTAGATGAAAG
1 GCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAG
* * * *
2669946 GCCTAAATGTGCGTTTGACAGAAAGGTGCCAATAATGCAAGTTGGATGAAAG
1 GCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAG
* * * * * *
2669998 GACTAACTATGCATTTGGCGGAAAAGTGTCAATAATGCAAGTTAGATGAAATATTAAAT
1 GCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGATG-------AAAG
* *
2670057 GCCTAACTGTGTATTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAA
1 GCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAA
2670108 AACAATGTAT
Statistics
Matches: 233, Mismatches: 27, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
52 126 0.54
53 63 0.27
59 44 0.19
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.25
Consensus pattern (52 bp):
GCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAG
Found at i:2670004 original size:104 final size:105
Alignment explanation
Indices: 2669728--2670048 Score: 385
Period size: 104 Copynumber: 3.0 Consensus size: 105
2669718 AAAGTTAAAT
* * * * *
2669728 GCCTAATTATGCATATT-AGCATAAAGGTGCCATTAATGCAAGTTAGATGATCAGTTAACTGCCT
1 GCCTAAATATGCATATTGA-CAGAAAGGTGCCAATAATGCAAGTTAGATG---A---AA-GGACT
*
2669792 AACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATAAAAG
58 AACTGTGCAT-TTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
* * *
2669841 GCCTAACTATGCATATTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGC
1 GCCTAAATATGCATATTGACAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGACTAACTGTGC
** *
2669906 ATTTGATAGAAAGGTGCCAATAATGCAAGTTAGATGAAAG
66 ATTTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
* * * *
2669946 GCCTAAATGTGCGT-TTGACAGAAAGGTGCCAATAATGCAAGTTGGATGAAAGGACTAACTATGC
1 GCCTAAATATGCATATTGACAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGACTAACTGTGC
* *
2670010 ATTTGGCGGAAAAGTGTCAATAATGCAAGTTAGATGAAA
66 ATTTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAA
2670049 TATTAAATGC
Statistics
Matches: 186, Mismatches: 21, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
104 80 0.43
105 45 0.24
106 14 0.08
107 2 0.01
110 1 0.01
113 44 0.24
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.26
Consensus pattern (105 bp):
GCCTAAATATGCATATTGACAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGACTAACTGTGC
ATTTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
Found at i:2676672 original size:60 final size:54
Alignment explanation
Indices: 2676587--2676907 Score: 343
Period size: 52 Copynumber: 6.0 Consensus size: 54
2676577 AAAGTTAAAT
* * * *
2676587 GCCTAATTGTGCATATTGGCAGAAAGGTGACATTAATGCAAGTTAGATGATCAGTTAAAT
1 GCCTAATTGTGCATATTGGTAGAAAGGTGCCAATAATGCAAGTTA-A-GAT--G--AAAG
* * * *
2676647 GCCTTACTGTGCATATTGGTAGAAAGGTGTCAATAACGCAAGTT-AGATGAAAG
1 GCCTAATTGTGCATATTGGTAGAAAGGTGCCAATAATGCAAGTTAAGATGAAAG
* *
2676700 GCCTGATTGTGAATATTGGTAGAAAGGTGCCAATAATGCAAGTTAA-ATGAAAG
1 GCCTAATTGTGCATATTGGTAGAAAGGTGCCAATAATGCAAGTTAAGATGAAAG
2676753 GCCTAATTGTGCAT-TTGGTAGAAAGGTGCCAATAATGCAAGTT-AGATGAAAG
1 GCCTAATTGTGCATATTGGTAGAAAGGTGCCAATAATGCAAGTTAAGATGAAAG
* * * * * * *
2676805 GCCTAATTGTGCAT-TTGGCATAAATGAGTCAATAATGCAAGTT-AGATTAATG
1 GCCTAATTGTGCATATTGGTAGAAAGGTGCCAATAATGCAAGTTAAGATGAAAG
* * * *
2676857 GTCTAACTGTGCAT-TTGGCAGAAAGGTGCCAACAATGCAAGTT-AGATGAAA
1 GCCTAATTGTGCATATTGGTAGAAAGGTGCCAATAATGCAAGTTAAGATGAAA
2676908 CGTTAAATGT
Statistics
Matches: 229, Mismatches: 30, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
51 1 0.00
52 123 0.54
53 61 0.27
54 1 0.00
55 1 0.00
57 3 0.01
58 1 0.00
60 38 0.17
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (54 bp):
GCCTAATTGTGCATATTGGTAGAAAGGTGCCAATAATGCAAGTTAAGATGAAAG
Found at i:2676744 original size:113 final size:107
Alignment explanation
Indices: 2676587--2676907 Score: 382
Period size: 104 Copynumber: 3.0 Consensus size: 107
2676577 AAAGTTAAAT
* * *
2676587 GCCTAATTGTGCATATTGGCAGAAAGGTGACATTAATGCAAGTTAGATGATCAGTTAAATGCCTT
1 GCCTAATTGTGCATATTGGCAGAAAGGTGACAATAATGCAAGTTAGAT-AT--G--AAAGGCCTA
*
2676652 ACTGTGCATATTGGTAGAAAGGTGTCAATAACGCAAGTTAGATGAAAG
61 ACTGTGCAT-TTGGTAGAAAGGTGCCAATAACGCAAGTTAGATGAAAG
* * * * *
2676700 GCCTGATTGTGAATATTGGTAGAAAGGTGCCAATAATGCAAGTTA-A-ATGAAAGGCCTAATTGT
1 GCCTAATTGTGCATATTGGCAGAAAGGTGACAATAATGCAAGTTAGATATGAAAGGCCTAACTGT
*
2676763 GCATTTGGTAGAAAGGTGCCAATAATGCAAGTTAGATGAAAG
66 GCATTTGGTAGAAAGGTGCCAATAACGCAAGTTAGATGAAAG
* * * * * *
2676805 GCCTAATTGTGCAT-TTGGCATAAATGAGTCAATAATGCAAGTTAGAT-T-AATGGTCTAACTGT
1 GCCTAATTGTGCATATTGGCAGAAAGGTGACAATAATGCAAGTTAGATATGAAAGGCCTAACTGT
* * *
2676867 GCATTTGGCAGAAAGGTGCCAACAATGCAAGTTAGATGAAA
66 GCATTTGGTAGAAAGGTGCCAATAACGCAAGTTAGATGAAA
2676908 CGTTAAATGT
Statistics
Matches: 184, Mismatches: 22, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
104 75 0.41
105 50 0.27
106 15 0.08
108 1 0.01
110 2 0.01
112 1 0.01
113 40 0.22
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (107 bp):
GCCTAATTGTGCATATTGGCAGAAAGGTGACAATAATGCAAGTTAGATATGAAAGGCCTAACTGT
GCATTTGGTAGAAAGGTGCCAATAACGCAAGTTAGATGAAAG
Found at i:2676791 original size:52 final size:52
Alignment explanation
Indices: 2676654--2676966 Score: 356
Period size: 52 Copynumber: 5.8 Consensus size: 52
2676644 AATGCCTTAC
* * *
2676654 TGTGCATATTGGTAGAAAGGTGTCAATAACGCAAGTTAGATGAAAGGCCTGAT
1 TGTGCAT-TTGGTAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGCCTAAT
* *
2676707 TGTGAATATTGGTAGAAAGGTGCCAATAATGCAAGTTAAATGAAAGGCCTAAT
1 TGTGCAT-TTGGTAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGCCTAAT
2676760 TGTGCATTTGGTAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGCCTAAT
1 TGTGCATTTGGTAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGCCTAAT
* * * * * * * * *
2676812 TGTGCATTTGGCATAAATGAGTCAATAATGCAAGTTAGATTAATGGTCTAAC
1 TGTGCATTTGGTAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGCCTAAT
* * * *
2676864 TGTGCATTTGGCAGAAAGGTGCCAACAATGCAAGTTAGATGAAACGTTAAATGTCTAAC
1 TGTGCATTTGGTAGAAAGGTGCCAATAATGCAAGTTAGATGAAA-G------GCCTAAT
* * *
2676923 TGTGGATTTGGAAGAAAGGTGCCACTAATGCAAGTTAGATGAAA
1 TGTGCATTTGGTAGAAAGGTGCCAATAATGCAAGTTAGATGAAA
2676967 AACAATGTAT
Statistics
Matches: 226, Mismatches: 27, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
52 124 0.55
53 55 0.24
59 47 0.21
ACGTcount: A:0.36, C:0.12, G:0.26, T:0.27
Consensus pattern (52 bp):
TGTGCATTTGGTAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGCCTAAT
Found at i:2676803 original size:27 final size:27
Alignment explanation
Indices: 2676721--2676805 Score: 79
Period size: 26 Copynumber: 3.2 Consensus size: 27
2676711 AATATTGGTA
*
2676721 GAAAGGTGCCAATAATGCAAGTTAAAT
1 GAAAGGTGCCAATAATGCAAGTTAGAT
** * *
2676748 GAAA-G-GCCTAATTGTGC-A-TTTGGT
1 GAAAGGTGCC-AATAATGCAAGTTAGAT
2676772 AGAAAGGTGCCAATAATGCAAGTTAGAT
1 -GAAAGGTGCCAATAATGCAAGTTAGAT
2676800 GAAAGG
1 GAAAGG
2676806 CCTAATTGTG
Statistics
Matches: 43, Mismatches: 9, Indels: 12
0.67 0.14 0.19
Matches are distributed among these distances:
24 3 0.07
25 8 0.19
26 14 0.33
27 14 0.33
28 4 0.09
ACGTcount: A:0.39, C:0.11, G:0.27, T:0.24
Consensus pattern (27 bp):
GAAAGGTGCCAATAATGCAAGTTAGAT
Found at i:2690197 original size:57 final size:56
Alignment explanation
Indices: 2690066--2690203 Score: 140
Period size: 57 Copynumber: 2.5 Consensus size: 56
2690056 TATTCCTTCA
* * * * *
2690066 TATTATTATTATTATTTTATTTC-TTATATTTTATTGTATATACATGTATTATTAC
1 TATTTTTAATATTATTTTATTTATTTATATGTTATTGTATATACATATATTATTAC
* * *
2690121 TATTTTTACTATT-TATTTATTTTATTTATATGTTATAT-TATATATATATATTATT-T
1 TATTTTTAATATTAT-TTTA-TTTATTTATATGTTAT-TGTATATACATATATTATTAC
2690177 TATTTCTTAATATTATTTTATTTATTT
1 TATTT-TTAATATTATTTTATTTATTT
2690204 TTTAGTTTAC
Statistics
Matches: 69, Mismatches: 8, Indels: 11
0.78 0.09 0.12
Matches are distributed among these distances:
54 1 0.01
55 15 0.22
56 15 0.22
57 36 0.52
58 2 0.03
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (56 bp):
TATTTTTAATATTATTTTATTTATTTATATGTTATTGTATATACATATATTATTAC
Found at i:2690304 original size:22 final size:23
Alignment explanation
Indices: 2690279--2690322 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
2690269 TTTGGTTTAT
2690279 TTATTTTATTGATTTAT-TTTTC
1 TTATTTTATTGATTTATATTTTC
*
2690301 TTATTTTATTTATTTATATTTT
1 TTATTTTATTGATTTATATTTT
2690323 TTCTTTATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.75
Consensus pattern (23 bp):
TTATTTTATTGATTTATATTTTC
Found at i:2690306 original size:13 final size:13
Alignment explanation
Indices: 2690274--2690346 Score: 53
Period size: 13 Copynumber: 5.5 Consensus size: 13
2690264 CTCGTTTTGG
2690274 TTTATTTATTTTA
1 TTTATTTATTTTA
*
2690287 TTGATTTATTTT-
1 TTTATTTATTTTA
2690299 TCTTATTT-TATTTA
1 T-TTATTTAT-TTTA
*
2690313 TTTATATT-TTTTC
1 TTTAT-TTATTTTA
* *
2690326 TTTATTCATCTTA
1 TTTATTTATTTTA
2690339 TTCTATTT
1 TT-TATTT
2690347 TGTCTTTATT
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
12 3 0.06
13 36 0.77
14 8 0.17
ACGTcount: A:0.19, C:0.07, G:0.01, T:0.73
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:2690330 original size:35 final size:35
Alignment explanation
Indices: 2690233--2690346 Score: 90
Period size: 35 Copynumber: 3.3 Consensus size: 35
2690223 TATATATTTA
* * *
2690233 TATTTTATTTCTTT-TATTTTATCTTT-TTTTCCT
1 TATTTTATTTATTTATATTTTTTCTTTATTTTTCT
** * **
2690266 CGTTTTGGTTTATTTAT-TTTATTGATTTATTTTTCT
1 TATTTT-ATTTATTTATATTT-TTTCTTTATTTTTCT
**
2690302 TATTTTATTTATTTATATTTTTTCTTTATTCATCT
1 TATTTTATTTATTTATATTTTTTCTTTATTTTTCT
*
2690337 TATTCTATTT
1 TATTTTATTT
2690347 TGTCTTTATT
Statistics
Matches: 60, Mismatches: 16, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
33 4 0.07
34 9 0.15
35 34 0.57
36 13 0.22
ACGTcount: A:0.16, C:0.09, G:0.04, T:0.72
Consensus pattern (35 bp):
TATTTTATTTATTTATATTTTTTCTTTATTTTTCT
Found at i:2690437 original size:4 final size:4
Alignment explanation
Indices: 2690428--2690453 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2690418 TTATCTGTTA
2690428 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
2690454 TCTCTTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:2692765 original size:16 final size:15
Alignment explanation
Indices: 2692744--2692773 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2692734 AAGATGGAAG
2692744 AGAAGATCAGGATGTT
1 AGAAGATCA-GATGTT
2692760 AGAAGATCAGATGT
1 AGAAGATCAGATGT
2692774 AGATGGTCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.40, C:0.07, G:0.30, T:0.23
Consensus pattern (15 bp):
AGAAGATCAGATGTT
Found at i:2693866 original size:95 final size:96
Alignment explanation
Indices: 2693694--2693956 Score: 352
Period size: 95 Copynumber: 2.7 Consensus size: 96
2693684 ATATTATAAT
* * * *
2693694 ATTATATATATACAATAAAGCTTAAGCTGTCCCTCTAAAGCAATTGGTTAAACACCCCGGCTTTA
1 ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACACCACGGCTTTA
*
2693759 TGGATAAGATTCAGTTAGCCTGATAAAGGTG
66 TGGATAAGATTCAGCTAGCCTGATAAAGGTG
* *
2693790 ATTATA-ATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCATGGCTTTA
1 ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACACCACGGCTTTA
* *
2693854 TTGATAATATTCAGCTAGCCTGATAAAGGTG
66 TGGATAAGATTCAGCTAGCCTGATAAAGGTG
* * * *
2693885 ATTATAATATTTATACAATGATA--TTGAGTTGTCCCTCTAGAGCAATTGGTTAAGCACCCCGAC
1 ATTAT-ATA--TATACAAT-AAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACACCACGGC
2693948 TTTATGGAT
62 TTTATGGAT
2693957 TCAGCTAGCC
Statistics
Matches: 146, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
95 85 0.58
96 7 0.05
97 1 0.01
98 43 0.29
99 8 0.05
100 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Consensus pattern (96 bp):
ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACACCACGGCTTTA
TGGATAAGATTCAGCTAGCCTGATAAAGGTG
Found at i:2695412 original size:34 final size:36
Alignment explanation
Indices: 2695283--2695433 Score: 225
Period size: 36 Copynumber: 4.2 Consensus size: 36
2695273 TAATTTACTC
2695283 AAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTT
1 AAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTT
* * *
2695320 AAAAAAAATTTTGTCTTTCTTGAGACAGTTTCTCGT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
* *
2695356 AAAACAAATTTTGTCTCTCTTGAGATATTTTCTCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
*
2695392 AAAACAAA-TTT-TCTCTCTTGAGACAGTTTCCCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
2695426 AAAACAAA
1 AAAACAAA
2695434 AACTTTGAAT
Statistics
Matches: 103, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
34 28 0.27
35 3 0.03
36 65 0.63
37 7 0.07
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.40
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
Found at i:2695546 original size:36 final size:36
Alignment explanation
Indices: 2695448--2695566 Score: 132
Period size: 36 Copynumber: 3.3 Consensus size: 36
2695438 TTGAATCAGT
* * *
2695448 TTTC-CTTGAAACAAATTTTGTCTCCCTTGAGATAG
1 TTTCTCTTGAACCAAATTTTGTCTCTCTTGAGACAG
* * * * * *
2695483 TTTCTTTTGGAACTAAGTTTTGGCTCTCTTTAGACAA
1 TTTCTCTT-GAACCAAATTTTGTCTCTCTTGAGACAG
2695520 TTTCTCTTGAACCAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAACCAAATTTTGTCTCTCTTGAGACAG
*
2695556 TTTCCCTTGAA
1 TTTCTCTTGAA
2695567 ACTAAATCTT
Statistics
Matches: 66, Mismatches: 16, Indels: 3
0.78 0.19 0.04
Matches are distributed among these distances:
35 4 0.06
36 35 0.53
37 27 0.41
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTCTCTTGAACCAAATTTTGTCTCTCTTGAGACAG
Found at i:2695578 original size:138 final size:137
Alignment explanation
Indices: 2695364--2695711 Score: 450
Period size: 138 Copynumber: 2.5 Consensus size: 137
2695354 GTAAAACAAA
* * * *
2695364 TTTTGTCTCTCTTGAGATATTTTCTCTTAAAACAAATTT-TCTCTCTTGAGACAGTTTCCCTTAA
1 TTTTGTCTCTCTTAAGATAATTTCTCTTGAAACAAATTTGTCTCTCTTGAGACAGTTTCCCTTGA
* * ** * *
2695428 AACAAAAACTTTGAATCA-GTTTTCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTTTCTTTTG
66 AACTAAATCTTTGAAT-ATGTTTTCCTTGAAACAAATTTCATCCCCCTTGAGATAGTTTATTTTG
*
2695492 GAACTAAG
130 AAACTAAG
* * * *
2695500 TTTTGGCTCTCTTTAGACAATTTCTCTTGAACCAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 TTTTGTCTCTCTTAAGATAATTTCTCTTGAAACAAA-TTTGTCTCTCTTGAGACAGTTTCCCTTG
*
2695565 AAACTAAATCTTTGAATATGTTTTCCTTGAAACAAATTTCATCCCCCTTGAGATATTTTATTTTG
65 AAACTAAATCTTTGAATATGTTTTCCTTGAAACAAATTTCATCCCCCTTGAGATAGTTTATTTTG
*
2695630 AAACTAAT
130 AAACTAAG
* **
2695638 TTTTGTCTCTCTTAAGATAATTT-TCCTTGAAACAAAATTTGTCTCCCTTGAGACAGTTTCTTTT
1 TTTTGTCTCTCTTAAGATAATTTCT-CTTGAAAC-AAATTTGTCTCTCTTGAGACAGTTTCCCTT
*
2695702 GGAACTAAAT
64 GAAACTAAAT
2695712 TTTTTCTCTC
Statistics
Matches: 183, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
136 30 0.16
137 5 0.03
138 145 0.79
139 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.11, T:0.43
Consensus pattern (137 bp):
TTTTGTCTCTCTTAAGATAATTTCTCTTGAAACAAATTTGTCTCTCTTGAGACAGTTTCCCTTGA
AACTAAATCTTTGAATATGTTTTCCTTGAAACAAATTTCATCCCCCTTGAGATAGTTTATTTTGA
AACTAAG
Found at i:2695668 original size:37 final size:37
Alignment explanation
Indices: 2695611--2695743 Score: 128
Period size: 37 Copynumber: 3.6 Consensus size: 37
2695601 TTTCATCCCC
* * *
2695611 CTTGAGATATTTTATTTTGAAACTAATTTTTGTCTCT
1 CTTGAGATAGTTTCTCTTGAAACTAATTTTTGTCTCT
* * ** *
2695648 CTTAAGATAATTT-TCCTTGAAAC-AAAATTTGTCTCC
1 CTTGAGATAGTTTCT-CTTGAAACTAATTTTTGTCTCT
* * *
2695684 CTTGAGACAGTTTCTTTTGGAACTAAATTTTT-TCTCT
1 CTTGAGATAGTTTCTCTTGAAACT-AATTTTTGTCTCT
2695721 CTTGAGATAGTTTCTCTTGAAAC
1 CTTGAGATAGTTTCTCTTGAAAC
2695744 ACAAAGAACC
Statistics
Matches: 75, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
36 27 0.36
37 43 0.57
38 5 0.07
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.46
Consensus pattern (37 bp):
CTTGAGATAGTTTCTCTTGAAACTAATTTTTGTCTCT
Found at i:2695708 original size:73 final size:73
Alignment explanation
Indices: 2695585--2695744 Score: 200
Period size: 73 Copynumber: 2.2 Consensus size: 73
2695575 TTTGAATATG
* *
2695585 TTTTCCTTGAAAC-AAATTTCATCCCCCTTGAGATATTTTATTTTGAAACT-AATTTTTGTCTCT
1 TTTTCCTTGAAACAAAATTTCATCCCCCTTGAGACAGTTTATTTTGAAACTAAATTTTT-TCTCT
2695648 CTTAAGATAA
65 CTTAAGAT-A
* * * *
2695658 TTTTCCTTGAAACAAAATTT-GTCTCCCTTGAGACAGTTTCTTTTGGAACTAAATTTTTTCTCTC
1 TTTTCCTTGAAACAAAATTTCATCCCCCTTGAGACAGTTTATTTTGAAACTAAATTTTTTCTCTC
*
2695722 TTGAGATA
66 TTAAGATA
*
2695730 GTTTCTCTTGAAACA
1 TTTTC-CTTGAAACA
2695745 CAAAGAACCT
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
72 5 0.07
73 58 0.76
74 13 0.17
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.44
Consensus pattern (73 bp):
TTTTCCTTGAAACAAAATTTCATCCCCCTTGAGACAGTTTATTTTGAAACTAAATTTTTTCTCTC
TTAAGATA
Found at i:2697563 original size:2 final size:2
Alignment explanation
Indices: 2697556--2697603 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
2697546 TTACAAGCTA
2697556 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
*
2697598 GT AT AT
1 AT AT AT
2697604 TTTATTTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2697645 original size:4 final size:4
Alignment explanation
Indices: 2697636--2697727 Score: 53
Period size: 4 Copynumber: 21.8 Consensus size: 4
2697626 CTCGTTTTGG
* * *
2697636 TTTA TTTA TTT- TATT- TTTA TTTTC TTTA TTTA TTGA TTTA TTTT TCTTA
1 TTTA TTTA TTTA T-TTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA T-TTA
* * *
2697685 TTTTA TTTA TTTA TATTT TTTC TTTA TTCA TCTTA TTCTA TTT
1 -TTTA TTTA TTTA T-TTA TTTA TTTA TTTA T-TTA TT-TA TTT
2697728 TGTCTTTATT
Statistics
Matches: 69, Mismatches: 11, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
3 3 0.04
4 47 0.68
5 18 0.26
6 1 0.01
ACGTcount: A:0.18, C:0.07, G:0.01, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:2697648 original size:9 final size:9
Alignment explanation
Indices: 2697636--2697702 Score: 56
Period size: 9 Copynumber: 7.8 Consensus size: 9
2697626 CTCGTTTTGG
2697636 TTTATTTAT
1 TTTATTTAT
2697645 TTTA--T-T
1 TTTATTTAT
2697651 TTTATTT-T
1 TTTATTTAT
2697659 CTTTATTTA-
1 -TTTATTTAT
*
2697668 TTGATTTAT
1 TTTATTTAT
2697677 TTT-TCTTAT
1 TTTAT-TTAT
2697686 TTTATTTAT
1 TTTATTTAT
2697695 TTATATTT
1 TT-TATTT
2697703 TTTCTTTATT
Statistics
Matches: 48, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
6 5 0.10
7 1 0.02
8 10 0.21
9 26 0.54
10 6 0.12
ACGTcount: A:0.19, C:0.03, G:0.01, T:0.76
Consensus pattern (9 bp):
TTTATTTAT
Found at i:2705903 original size:19 final size:17
Alignment explanation
Indices: 2705861--2705903 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 17
2705851 TTAAGACATT
2705861 AATATTTTTAATAAATA
1 AATATTTTTAATAAATA
2705878 ATTATATTTTTATATTAAATA
1 A--ATATTTTTA-A-TAAATA
2705899 AATAT
1 AATAT
2705904 CTAACTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 1 0.05
19 13 0.59
20 1 0.05
21 7 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AATATTTTTAATAAATA
Found at i:2716711 original size:44 final size:43
Alignment explanation
Indices: 2716663--2716803 Score: 113
Period size: 44 Copynumber: 3.2 Consensus size: 43
2716653 CTAATCTACT
* *
2716663 TCCTTTTGTGATAGAATCGAGCAAAAAGTTGACGATGATCCAAC
1 TCCTTATGTGATAGAATCGAGCAAAAAGTTGATG-TGATCCAAC
* * * * * * * * *
2716707 TCCTTATGCGATGGATTTGAACGAAATGAAT-ATGTCGATCCACC
1 TCCTTATGTGATAGAATCGAGCAAAAAG-TTGATGT-GATCCAAC
** *
2716751 TCCTCCTGTGATAGAATCGAGCAAAAAATTGATGCTGATCCAAC
1 TCCTTATGTGATAGAATCGAGCAAAAAGTTGATG-TGATCCAAC
2716795 TCCTTATGT
1 TCCTTATGT
2716804 AATGGATTTG
Statistics
Matches: 68, Mismatches: 25, Indels: 8
0.67 0.25 0.08
Matches are distributed among these distances:
43 2 0.03
44 64 0.94
45 2 0.03
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (43 bp):
TCCTTATGTGATAGAATCGAGCAAAAAGTTGATGTGATCCAAC
Found at i:2716761 original size:88 final size:88
Alignment explanation
Indices: 2716669--2716856 Score: 286
Period size: 88 Copynumber: 2.1 Consensus size: 88
2716659 TACTTCCTTT
* *
2716669 TGTGATAGAATCGAGCAAAAAGTTGACGATGATCCAACTCCTTATGCGATGGATTTGAACGAAAT
1 TGTGATAGAATCGAGCAAAAAATTGACGATGATCCAACTCCTTATGCAATGGATTTGAACGAAAT
* *
2716734 GAATATGTCGATCCACCTCCTCC
66 AAAAATGTCGATCCACCTCCTCC
* * *
2716757 TGTGATAGAATCGAGCAAAAAATTGATGCTGATCCAACTCCTTATGTAATGGATTTGAACGAAAT
1 TGTGATAGAATCGAGCAAAAAATTGACGATGATCCAACTCCTTATGCAATGGATTTGAACGAAAT
* *
2716822 AAAAATGTTGATCCACCTCCTTC
66 AAAAATGTCGATCCACCTCCTCC
*
2716845 TGTGATGGAATC
1 TGTGATAGAATC
2716857 AAATGATATG
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 90 1.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (88 bp):
TGTGATAGAATCGAGCAAAAAATTGACGATGATCCAACTCCTTATGCAATGGATTTGAACGAAAT
AAAAATGTCGATCCACCTCCTCC
Found at i:2716834 original size:44 final size:44
Alignment explanation
Indices: 2716698--2716853 Score: 136
Period size: 44 Copynumber: 3.5 Consensus size: 44
2716688 AAGTTGACGA
* * *
2716698 TGATCCAACTCCTTATGCGATGGATTTGAACGAAATGAATATGT
1 TGATCCAACTCCTTATGTGATGGATTTGAACGAAATAAAAATGT
* * ** * * * * * *
2716742 CGATCCACCTCCTCCTGTGATAGAATCGAGC-AAA-AAATTGATGC
1 TGATCCAACTCCTTATGTGATGGATTTGAACGAAATAAA--AATGT
*
2716786 TGATCCAACTCCTTATGTAATGGATTTGAACGAAATAAAAATGT
1 TGATCCAACTCCTTATGTGATGGATTTGAACGAAATAAAAATGT
* *
2716830 TGATCCACCTCCTTCTGTGATGGA
1 TGATCCAACTCCTTATGTGATGGA
2716854 ATCAAATGAT
Statistics
Matches: 82, Mismatches: 26, Indels: 8
0.71 0.22 0.07
Matches are distributed among these distances:
42 2 0.02
43 3 0.04
44 71 0.87
45 3 0.04
46 3 0.04
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (44 bp):
TGATCCAACTCCTTATGTGATGGATTTGAACGAAATAAAAATGT
Found at i:2716835 original size:132 final size:131
Alignment explanation
Indices: 2716698--2716942 Score: 307
Period size: 132 Copynumber: 1.9 Consensus size: 131
2716688 AAGTTGACGA
* **
2716698 TGATCCAACTCCTTATGCGATGGATTTGAACGAAATGAAT-A-TG-TCGATCCACCTCCTCCTGT
1 TGATCCAACTCCTTATGCGATGGAATCAAACGAAATG--TCAGTGCT-GATCCACCTCCTCCTGT
* *
2716760 GATAGAATCGAGCAAAAAATTGATGCTGATCCAACTCCTTATGTAATGGATTTGAACGAAATAAA
63 GATAGAATCGAGC-AAAAATTGATGCTGATCCAACTCCGTATGCAATGGATTTGAACGAAATAAA
2716825 AATGT
127 AATGT
* * * * * * * *
2716830 TGATCCACCTCCTTCTGTGATGGAATCAAATGATATGTCAGTGCTGATCTACCTTCTTCTGTGAT
1 TGATCCAACTCCTTATGCGATGGAATCAAACGAAATGTCAGTGCTGATCCACCTCCTCCTGTGAT
*
2716895 AGAATCGAGCAAAAATTGATGCTGATCCAACTCCGTATGCGATGGATT
66 AGAATCGAGCAAAAATTGATGCTGATCCAACTCCGTATGCAATGGATT
2716943 AGCCAAGTAT
Statistics
Matches: 96, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
130 1 0.01
131 36 0.38
132 58 0.60
133 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (131 bp):
TGATCCAACTCCTTATGCGATGGAATCAAACGAAATGTCAGTGCTGATCCACCTCCTCCTGTGAT
AGAATCGAGCAAAAATTGATGCTGATCCAACTCCGTATGCAATGGATTTGAACGAAATAAAAATG
T
Found at i:2717061 original size:96 final size:96
Alignment explanation
Indices: 2716917--2717090 Score: 285
Period size: 96 Copynumber: 1.8 Consensus size: 96
2716907 AAATTGATGC
* *
2716917 TGATCCAACTCCGTATGCGATGGATTAGCCAAGTATTGGTGTCATTCCAACTCCGTATGTGAAAG
1 TGATCCAACTCCGTATGCGATGGATGAGCCAAGTATTGGTGTCATTCCAACTCAGTATGTGAAAG
2716982 AATCAAGCAAGAATGACAATGTTGATGATAT
66 AATCAAGCAAGAATGACAATGTTGATGATAT
* ** *
2717013 TGATCCAACTCCGTATGCTATGGATGAGCCAAGTATTGGTGTTGTTCCAACTCAGTATGTGAAGG
1 TGATCCAACTCCGTATGCGATGGATGAGCCAAGTATTGGTGTCATTCCAACTCAGTATGTGAAAG
*
2717078 AATCGAGCAAGAA
66 AATCAAGCAAGAA
2717091 GGAACAAGTT
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
96 71 1.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.28
Consensus pattern (96 bp):
TGATCCAACTCCGTATGCGATGGATGAGCCAAGTATTGGTGTCATTCCAACTCAGTATGTGAAAG
AATCAAGCAAGAATGACAATGTTGATGATAT
Found at i:2717526 original size:36 final size:36
Alignment explanation
Indices: 2717480--2717599 Score: 87
Period size: 36 Copynumber: 3.3 Consensus size: 36
2717470 GTTTCAAGGG
* *
2717480 AAAACTATCTCAAGCGAGACAAAGTTGGTTTTAAGA
1 AAAACCATCTCAAGCGAGACAAAGTTAGTTTTAAGA
* * * * * * * *
2717516 AAAACCATCTCGAGTGAGATACATTTTGTTTCAAGGG
1 AAAACCATCTCAAGCGAGACAAAGTTAGTTTTAA-GA
*** * * *
2717553 AAAGTTATTTCAAGCGAGACGAAGTTATTTTTAAGA
1 AAAACCATCTCAAGCGAGACAAAGTTAGTTTTAAGA
2717589 AAAACCATCTC
1 AAAACCATCTC
2717600 GAGTGAGATA
Statistics
Matches: 56, Mismatches: 27, Indels: 2
0.66 0.32 0.02
Matches are distributed among these distances:
36 34 0.61
37 22 0.39
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (36 bp):
AAAACCATCTCAAGCGAGACAAAGTTAGTTTTAAGA
Found at i:2717568 original size:73 final size:76
Alignment explanation
Indices: 2717447--2717627 Score: 278
Period size: 73 Copynumber: 2.4 Consensus size: 76
2717437 AGAGAAGCTC
*
2717447 TCTCGAGTGAGATAAAATTTCTTGTTTCAAGGGAAAACTATCTCAAGCGAGACAAAGTTGGTTTT
1 TCTCGAGTGAGATAAAATTTCTTGTTTCAAGGGAAAACTATCTCAAGCGAGACAAAGTTAGTTTT
2717512 AAGAAAAACCA
66 AAGAAAAACCA
* ** * * *
2717523 TCTCGAGTGAGAT-ACA-TT-TTGTTTCAAGGGAAAGTTATTTCAAGCGAGACGAAGTTATTTTT
1 TCTCGAGTGAGATAAAATTTCTTGTTTCAAGGGAAAACTATCTCAAGCGAGACAAAGTTAGTTTT
2717585 AAGAAAAACCA
66 AAGAAAAACCA
2717596 TCTCGAGTGAGATAAAATTTCTTGTTTCAAGG
1 TCTCGAGTGAGATAAAATTTCTTGTTTCAAGG
2717628 AAATCTCAAG
Statistics
Matches: 94, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
73 62 0.66
74 4 0.04
75 4 0.04
76 24 0.26
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.31
Consensus pattern (76 bp):
TCTCGAGTGAGATAAAATTTCTTGTTTCAAGGGAAAACTATCTCAAGCGAGACAAAGTTAGTTTT
AAGAAAAACCA
Found at i:2717641 original size:35 final size:32
Alignment explanation
Indices: 2717595--2717659 Score: 85
Period size: 35 Copynumber: 1.9 Consensus size: 32
2717585 AAGAAAAACC
*
2717595 ATCTCGAGTGAGATAAAATTTCTTGTTTCAAGGAA
1 ATCTCAAGTGAGA-AAAA-TT-TTGTTTCAAGGAA
*
2717630 ATCTCAAGTGAGAAACATTTTGTTTCAAGG
1 ATCTCAAGTGAGAAAAATTTTGTTTCAAGG
2717660 GAAAGTTGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 11 0.39
33 2 0.07
34 3 0.11
35 12 0.43
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (32 bp):
ATCTCAAGTGAGAAAAATTTTGTTTCAAGGAA
Found at i:2717674 original size:108 final size:109
Alignment explanation
Indices: 2717522--2717740 Score: 359
Period size: 108 Copynumber: 2.0 Consensus size: 109
2717512 AAGAAAAACC
* * * * *
2717522 ATCTCGAGTGAGATACATTTTGTTTCAAGGGAAAGTTATTTCAAGCGAGACGAAGTTATTTTTAA
1 ATCTCAAGTGAGAAACATTTTGTTTCAAGGGAAAGTTATCTCAAGCGAGACAAAGTTAGTTTTAA
2717587 GAAAAACCATCTCGAGTGAGATAAAATTTCTTGTTTC-AAGGAA
66 GAAAAACCATCTCGAGTGAGATAAAATTTCTTGTTTCAAAGGAA
* *
2717630 ATCTCAAGTGAGAAACATTTTGTTTCAAGGGAAAGTTGTCTCAAGCGAGACAAAGTTGGTTTTAA
1 ATCTCAAGTGAGAAACATTTTGTTTCAAGGGAAAGTTATCTCAAGCGAGACAAAGTTAGTTTTAA
*
2717695 GAAAAGCCATCTCGAGTGAGATAAAATTTCTTGTTTCAAAGGAA
66 GAAAAACCATCTCGAGTGAGATAAAATTTCTTGTTTCAAAGGAA
2717739 AT
1 AT
2717741 TTTCTCAAGA
Statistics
Matches: 102, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
108 94 0.92
109 8 0.08
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (109 bp):
ATCTCAAGTGAGAAACATTTTGTTTCAAGGGAAAGTTATCTCAAGCGAGACAAAGTTAGTTTTAA
GAAAAACCATCTCGAGTGAGATAAAATTTCTTGTTTCAAAGGAA
Found at i:2717847 original size:36 final size:35
Alignment explanation
Indices: 2717792--2717950 Score: 201
Period size: 36 Copynumber: 4.4 Consensus size: 35
2717782 AAATATTTTA
*
2717792 TGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAACT
1 TGTTTCAAG-GAAACTGTCTCAAGAGAGACAAAACT
*
2717828 TGTTTCAAGGTAAACTGTCTCAAGGGAGACAAAACT
1 TGTTTCAAGG-AAACTGTCTCAAGAGAGACAAAACT
* * *
2717864 TGTTTCCAAGGAAACTGTATCAAGAGAGATAAAATT
1 TGTTT-CAAGGAAACTGTCTCAAGAGAGACAAAACT
* * *
2717900 TGTTTCAATAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAA-GGAAACTGTCTCAAGAGAGACAAAACT
2717936 TGTTTCAAGGGAAAC
1 TGTTTCAA-GGAAAC
2717951 ATATTCAAAG
Statistics
Matches: 108, Mismatches: 12, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
35 4 0.04
36 99 0.92
37 5 0.05
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.26
Consensus pattern (35 bp):
TGTTTCAAGGAAACTGTCTCAAGAGAGACAAAACT
Found at i:2717969 original size:29 final size:29
Alignment explanation
Indices: 2717934--2718072 Score: 163
Period size: 29 Copynumber: 4.6 Consensus size: 29
2717924 GGAGACAAAA
*
2717934 TTTGTTTCAAGGGAAACATATTCAAAGAT
1 TTTGTTTCAAGGGAAACAGATTCAAAGAT
* *
2717963 TTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACGAAA
1 TTTGTTTCAAGGGAAACAGAT-TC---A-A-A-G-AT
*
2717999 TTTGTTTAAAGGGAAACAGATTCAAAGAT
1 TTTGTTTCAAGGGAAACAGATTCAAAGAT
2718028 TTTGTTTCAAGGGAAACAGATTCAAAGAT
1 TTTGTTTCAAGGGAAACAGATTCAAAGAT
2718057 TTTGTTTCAAGGGAAA
1 TTTGTTTCAAGGGAAA
2718073 TTGTCTCAAG
Statistics
Matches: 94, Mismatches: 7, Indels: 18
0.79 0.06 0.15
Matches are distributed among these distances:
28 1 0.01
29 64 0.68
30 1 0.01
31 1 0.01
32 2 0.02
33 2 0.02
34 1 0.01
35 1 0.01
36 20 0.21
37 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (29 bp):
TTTGTTTCAAGGGAAACAGATTCAAAGAT
Found at i:2718002 original size:65 final size:65
Alignment explanation
Indices: 2717898--2718044 Score: 240
Period size: 65 Copynumber: 2.3 Consensus size: 65
2717888 AGAGATAAAA
** * * *
2717898 TTTGTTTCAATAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACATATTCAAAGAT
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGGGAAACAGATTCAAAGAT
*
2717963 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTTGTTTAAAGGGAAACAGATTCAAAGAT
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGGGAAACAGATTCAAAGAT
2718028 TTTGTTTCAAGGGAAAC
1 TTTGTTTCAAGGGAAAC
2718045 AGATTCAAAG
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 76 1.00
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (65 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGGGAAACAGATTCAAAGAT
Found at i:2718116 original size:36 final size:36
Alignment explanation
Indices: 2718057--2718170 Score: 129
Period size: 36 Copynumber: 3.2 Consensus size: 36
2718047 ATTCAAAGAT
* *
2718057 TTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGAAAATTGTCTCAAGTGAGACAAAA
* ** ** *
2718093 TTTGTTTCAAAGAAAATAATCTCAAGTGAGATTAAT
1 TTTGTTTCAAGGAAAATTGTCTCAAGTGAGACAAAA
* *
2718129 TTTGTTTTAAGGAAAATTGTCTCCAGTGAGACAAAA
1 TTTGTTTCAAGGAAAATTGTCTCAAGTGAGACAAAA
*
2718165 ATTGTT
1 TTTGTT
2718171 CTTTGGGAAA
Statistics
Matches: 61, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
36 61 1.00
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (36 bp):
TTTGTTTCAAGGAAAATTGTCTCAAGTGAGACAAAA
Found at i:2718207 original size:73 final size:72
Alignment explanation
Indices: 2718055--2718208 Score: 184
Period size: 72 Copynumber: 2.1 Consensus size: 72
2718045 AGATTCAAAG
* *
2718055 ATTTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAAGAAAATAATCTCAAGT
1 ATTTTGTTTCAAGGAAAATTGTCTCAAGAGAGACAAAAATTGTTTCAAAGAAAATAATCTCAAGT
*
2718120 GAGATTA
66 GAGATCA
* * * **** *
2718127 ATTTTGTTTTAAGGAAAATTGTCTCCAGTGAGACAAAAATTGTTCTTTGGGAAAACT-ATCTCAT
1 ATTTTGTTTCAAGGAAAATTGTCTCAAGAGAGACAAAAATTGTT-TCAAAGAAAA-TAATCTCAA
2718191 GTGAGATCA
64 GTGAGATCA
2718200 ATTTTGTTT
1 ATTTTGTTT
2718209 GAAAGATTTC
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
72 39 0.57
73 29 0.42
74 1 0.01
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.36
Consensus pattern (72 bp):
ATTTTGTTTCAAGGAAAATTGTCTCAAGAGAGACAAAAATTGTTTCAAAGAAAATAATCTCAAGT
GAGATCA
Found at i:2719438 original size:15 final size:15
Alignment explanation
Indices: 2719418--2719450 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2719408 TGAGACATTA
*
2719418 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
2719433 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
2719448 CCC
1 CCC
2719451 ACCTAGTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.70, G:0.15, T:0.06
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:2720709 original size:20 final size:20
Alignment explanation
Indices: 2720684--2720737 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
2720674 GTTTGATCGA
2720684 TTTTCTTTCTTCTTTTATTT
1 TTTTCTTTCTTCTTTTATTT
2720704 TTTTCTTTCTT-TTTT-TTT
1 TTTTCTTTCTTCTTTTATTT
*
2720722 CTTT-TTT-TTCTTTTAT
1 TTTTCTTTCTTCTTTTAT
2720738 ATCTATCTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
16 2 0.06
17 7 0.23
18 7 0.23
19 4 0.13
20 11 0.35
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTTCTTTCTTCTTTTATTT
Found at i:2720711 original size:13 final size:12
Alignment explanation
Indices: 2720693--2720735 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
2720683 ATTTTCTTTC
2720693 TTCTTTTATTTTT
1 TTCTTTT-TTTTT
*
2720706 TTCTTTCTTTTT
1 TTCTTTTTTTTT
*
2720718 TT-TTCTTTTTT
1 TTCTTTTTTTTT
2720729 TTCTTTT
1 TTCTTTT
2720736 ATATCTATCT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
11 9 0.36
12 10 0.40
13 6 0.24
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (12 bp):
TTCTTTTTTTTT
Found at i:2720720 original size:14 final size:13
Alignment explanation
Indices: 2720693--2720735 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 13
2720683 ATTTTCTTTC
*
2720693 TTCTTTTATTTTT
1 TTCTTTTTTTTTT
2720706 TTCTTTCTTTTTTT
1 TTCTTT-TTTTTTT
2720720 TTCTTTTTTTTCTT
1 TTCTTTTTTTT-TT
2720734 TT
1 TT
2720736 ATATCTATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (13 bp):
TTCTTTTTTTTTT
Found at i:2720726 original size:9 final size:9
Alignment explanation
Indices: 2720693--2720735 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
2720683 ATTTTCTTTC
*
2720693 TTCTTTTAT
1 TTCTTTTTT
*
2720702 TT-TTTTCT
1 TTCTTTTTT
2720710 TTCTTTTTTT
1 TTC-TTTTTT
2720720 TTCTTTTTT
1 TTCTTTTTT
2720729 TTCTTTT
1 TTCTTTT
2720736 ATATCTATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 7 0.23
9 15 0.50
10 8 0.27
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:2720744 original size:4 final size:4
Alignment explanation
Indices: 2720737--2720769 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
2720727 TTTTCTTTTA
2720737 TATC TATC TATC TATC TATC TATC TATC TATC T
1 TATC TATC TATC TATC TATC TATC TATC TATC T
2720770 TCCTTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (4 bp):
TATC
Found at i:2721088 original size:2 final size:2
Alignment explanation
Indices: 2721041--2721079 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
2721031 GGACAACAAG
* * *
2721041 AT AT AT AT AT AT AT AT AT TT AT TT AT TT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2721080 CACATATATT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
AT
Found at i:2721455 original size:15 final size:15
Alignment explanation
Indices: 2721435--2721466 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2721425 TAAAGTCGTT
2721435 ATTCTAAAAAAGGTA
1 ATTCTAAAAAAGGTA
2721450 ATTCTAAAAAAGGTA
1 ATTCTAAAAAAGGTA
2721465 AT
1 AT
2721467 ATCATGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.28
Consensus pattern (15 bp):
ATTCTAAAAAAGGTA
Found at i:2722651 original size:149 final size:149
Alignment explanation
Indices: 2722369--2722666 Score: 357
Period size: 149 Copynumber: 2.0 Consensus size: 149
2722359 TCGTTTTCAA
* * * * * *
2722369 AGCTTCTACTTCATCTCCTACTTTTAGAAATATTTCTAACTGGTTCATGATCTTCAACTGTTGGC
1 AGCTCCTACATCATCTCCTACTTTCAGAAATATTTCGAACTGGTTCATGATCTTAAACTGTCGGC
** * * * * * * *
2722434 TTCAGCATTGAATCTTCTTGAGTCCACCTTGTTACTTCAACAGGCAAATGTCTGGATCGTCTCTT
66 TTCAGCATCAAATCATCTCGAGTCCAACTTGTTACCTCAACAGGCAAAGGTCTAGATCGTCTCCT
2722499 TGGT-AGATAGACTCCCTCT
131 TGGTAAG-TAGACTCCCTCT
* * * *
2722518 AGCTCCTACATCATCTCCTA-TTTCCAGAAATCTTTCGAGCTGGTTCGTGATCTTAAATTGTCGG
1 AGCTCCTACATCATCTCCTACTTT-CAGAAATATTTCGAACTGGTTCATGATCTTAAACTGTCGG
** * *
2722582 CTTCAGTGTCAAATCATCTCGAGTCCAACTTGTTACCTCAGCATGCAAAGGTCTAGATCGTCTCC
65 CTTCAGCATCAAATCATCTCGAGTCCAACTTGTTACCTCAACAGGCAAAGGTCTAGATCGTCTCC
2722647 TTGGTAAGTAGACTCCCTCT
130 TTGGTAAGTAGACTCCCTCT
2722667 TGACGCTACT
Statistics
Matches: 124, Mismatches: 23, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
148 3 0.02
149 119 0.96
150 2 0.02
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.36
Consensus pattern (149 bp):
AGCTCCTACATCATCTCCTACTTTCAGAAATATTTCGAACTGGTTCATGATCTTAAACTGTCGGC
TTCAGCATCAAATCATCTCGAGTCCAACTTGTTACCTCAACAGGCAAAGGTCTAGATCGTCTCCT
TGGTAAGTAGACTCCCTCT
Found at i:2725060 original size:18 final size:18
Alignment explanation
Indices: 2725039--2725073 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2725029 ACCGGTCATA
* *
2725039 ACCCGTTGACCCGACCCG
1 ACCCGTTAAACCGACCCG
2725057 ACCCGTTAAACCGACCC
1 ACCCGTTAAACCGACCC
2725074 AATCGTTGAC
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:0.23, C:0.49, G:0.17, T:0.11
Consensus pattern (18 bp):
ACCCGTTAAACCGACCCG
Found at i:2725153 original size:29 final size:29
Alignment explanation
Indices: 2725121--2725272 Score: 143
Period size: 29 Copynumber: 5.3 Consensus size: 29
2725111 ATTCGGTTTT
*
2725121 GGTGCTATTCTGGGAATTAATTCAAAATG
1 GGTGCTATTTTGGGAATTAATTCAAAATG
* *
2725150 GGTGCTATTTTGGTAATT-TTTCGAAAAT-
1 GGTGCTATTTTGGGAATTAATTC-AAAATG
* *
2725178 --TGATATTTTGGGAATTAATTCAAAATT
1 GGTGCTATTTTGGGAATTAATTCAAAATG
*
2725205 GGTGCTATTTTGAGAATTAATTCGAAAA-G
1 GGTGCTATTTTGGGAATTAATTC-AAAATG
* * * * **
2725234 GGTGCTAGTTTGGTAATTATTTTAAAAAA
1 GGTGCTATTTTGGGAATTAATTCAAAATG
2725263 GGTGCTATTT
1 GGTGCTATTT
2725273 GTGTAAAATG
Statistics
Matches: 100, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
26 19 0.19
27 3 0.03
28 7 0.07
29 67 0.67
30 4 0.04
ACGTcount: A:0.31, C:0.07, G:0.22, T:0.41
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTAATTCAAAATG
Found at i:2729228 original size:64 final size:64
Alignment explanation
Indices: 2729115--2729324 Score: 196
Period size: 64 Copynumber: 3.2 Consensus size: 64
2729105 TGCACTAAGA
* * *
2729115 GTGCATCGATGCATGAAGTGCATTCGATGTTTGAA--AAAT-AGCCTGGTGCATCGATGCATGGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAG---AGTGCATCGATGCATGGA
2729177 TT
63 TT
* * **
2729179 GTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATCAGAGTGCATCGATGCATGGAGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAGAGTGCATCGATGCATGGATT
* * * * *
2729243 GTGCATCGGTTCATGGAATGCATTCGACGTTTCAACTT-ATTCATTGA-TGCATCGATGCATGGT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAA-TTAAATCA--GAGTGCATCGATGCATGG-
2729306 ATT
62 ATT
*
2729309 GATGCATCGGTGCATG
1 G-TGCATCGATGCATG
2729325 CCTTTGAAAA
Statistics
Matches: 122, Mismatches: 16, Indels: 13
0.81 0.11 0.09
Matches are distributed among these distances:
64 82 0.67
65 17 0.14
66 8 0.07
67 15 0.12
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAGAGTGCATCGATGCATGGATT
Found at i:2729311 original size:21 final size:21
Alignment explanation
Indices: 2729285--2729324 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2729275 CAACTTATTC
2729285 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
2729306 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
2729325 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:2737772 original size:18 final size:17
Alignment explanation
Indices: 2737718--2737766 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
2737708 TTGGACTCCT
* *
2737718 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
2737736 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
2737754 AGTGCATTCGATG
1 AGTGCA-TCGATG
2737767 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:2737851 original size:64 final size:65
Alignment explanation
Indices: 2737738--2737945 Score: 207
Period size: 64 Copynumber: 3.2 Consensus size: 65
2737728 TGCACTAAGA
* * *
2737738 GTGCATCGATGCATGAAGTGCATTCGATGTTTGAA--AAAT-AGCCTGGTGCATCGATGCATGGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAG--TCGTGCATCGATGCATGGA
2737800 TT
64 TT
* * **
2737802 GTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATCAGT-GTGCATCGATGCATGGAGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAGTCGTGCATCGATGCATGGATT
* * *
2737866 GTG-ATCGGTGCATGGAATGCATTCGAT-TTTCAACTT-ATTCA-TCGATGCATCGATGCATGGT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAA-TTAAATCAGTCG-TGCATCGATGCATGG-
2737927 ATT
63 ATT
*
2737930 GATGCATCGGTGCATG
1 G-TGCATCGATGCATG
2737946 CCTTTGAAAA
Statistics
Matches: 123, Mismatches: 12, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
61 1 0.01
62 10 0.08
63 38 0.31
64 54 0.44
65 3 0.02
66 15 0.12
67 2 0.02
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAGTCGTGCATCGATGCATGGATT
Found at i:2741487 original size:15 final size:15
Alignment explanation
Indices: 2741467--2741502 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
2741457 TGACAATGAA
2741467 GATGATTTTGTGTTT
1 GATGATTTTGTGTTT
2741482 GATGATTTTGTGTTT
1 GATGATTTTGTGTTT
2741497 GATGAT
1 GATGAT
2741503 GGTGAGTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.17, C:0.00, G:0.28, T:0.56
Consensus pattern (15 bp):
GATGATTTTGTGTTT
Found at i:2746975 original size:29 final size:31
Alignment explanation
Indices: 2746930--2746994 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 31
2746920 AAACTTAATT
* *
2746930 AAAAAAGAATTAAAAC-A-ATAATATAAAAA
1 AAAAAAGAATAAAAACAACATAAAATAAAAA
2746959 AAAAAAGAA-AAATAACAACATAAAATAAAAA
1 AAAAAAGAATAAA-AACAACATAAAATAAAAA
*
2746990 TAAAA
1 AAAAA
2746995 TAAACCTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 2 0.07
29 12 0.40
30 1 0.03
31 15 0.50
ACGTcount: A:0.78, C:0.05, G:0.03, T:0.14
Consensus pattern (31 bp):
AAAAAAGAATAAAAACAACATAAAATAAAAA
Found at i:2747084 original size:25 final size:22
Alignment explanation
Indices: 2747055--2747108 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
2747045 AAAATGTAAG
2747055 AAAATAAAAGTTAGTAGCTAAATC
1 AAAATAAAA--TAGTAGCTAAATC
*
2747079 AGAAAT-AAATAGTAGCTAAATT
1 A-AAATAAAATAGTAGCTAAATC
2747101 AAAATAAA
1 AAAATAAA
2747109 TTAAAATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 4 0.15
22 15 0.56
24 4 0.15
25 4 0.15
ACGTcount: A:0.59, C:0.06, G:0.11, T:0.24
Consensus pattern (22 bp):
AAAATAAAATAGTAGCTAAATC
Found at i:2747094 original size:22 final size:21
Alignment explanation
Indices: 2747066--2747109 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
2747056 AAATAAAAGT
2747066 TAGTAGCTAAATCAGAAATAAA
1 TAGTAGCTAAATCA-AAATAAA
*
2747088 TAGTAGCTAAATTAAAATAAA
1 TAGTAGCTAAATCAAAATAAA
2747109 T
1 T
2747110 TAAAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.55, C:0.07, G:0.11, T:0.27
Consensus pattern (21 bp):
TAGTAGCTAAATCAAAATAAA
Found at i:2748486 original size:3 final size:3
Alignment explanation
Indices: 2748478--2748524 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
2748468 GTTTGGTTTG
* * *
2748478 TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TAA TAA CAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2748525 TAGATAGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2748966 original size:91 final size:91
Alignment explanation
Indices: 2748812--2749263 Score: 663
Period size: 91 Copynumber: 5.0 Consensus size: 91
2748802 GAAACGAGCT
* * *
2748812 AAGGTTGAAAAAGTTCTTCTCATTATGAACTTATTCTCCCTTGTTGGATGAGTTATTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTGTTGGATGAGTTCTTCTCATTAT
* * *
2748877 AAACTCTCCACTGGAAATGTTGATGT
66 GAACTCTCCACTGGAAATGTTGAGGC
* *
2748903 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTGTCGGATGAGTTGTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTGTTGGATGAGTTCTTCTCATTAT
* *
2748968 GAACTCCCCACTGGAAATGTTAAGGC
66 GAACTCTCCACTGGAAATGTTGAGGC
* * * *
2748994 AAGTTTGAACAAGTTTTTCTTATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTGTTGGATGAGTTCTTCTCATTAT
* * * **
2749059 TAACTCTTCACTGAAAATGTTGATCC
66 GAACTCTCCACTGGAAATGTTGAGGC
* * *
2749085 AAGGCTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTTGTCGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTGTTGGATGAGTTCTTCTCATTAT
2749150 GAACTC-CTCACTGGAAATGTTGAGGC
66 GAACTCTC-CACTGGAAATGTTGAGGC
* * *
2749176 ATGGTTGAACAAGTTCTTCTCATTATTAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTGTTGGATGAGTTCTTCTCATTAT
2749241 GAACTCTCCACTGGAAATGTTGA
66 GAACTCTCCACTGGAAATGTTGA
2749264 CTGGTTTATC
Statistics
Matches: 319, Mismatches: 40, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
91 318 1.00
92 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (91 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTGTTGGATGAGTTCTTCTCATTAT
GAACTCTCCACTGGAAATGTTGAGGC
Found at i:2751378 original size:7 final size:7
Alignment explanation
Indices: 2751316--2751497 Score: 190
Period size: 7 Copynumber: 24.9 Consensus size: 7
2751306 CAAAAAAATC
2751316 TTTTCTT
1 TTTTCTT
2751323 TTATT-TT
1 TT-TTCTT
2751330 TCTTTCTTT
1 T-TTTC-TT
2751339 TCTTTCTTT
1 T-TTTC-TT
2751348 TCTTTCTT
1 T-TTTCTT
2751356 TTCTTCTT
1 TT-TTCTT
*
2751364 TTGT-TT
1 TTTTCTT
2751370 TTTTCTT
1 TTTTCTT
2751377 TTTT-TT
1 TTTTCTT
*
2751383 ATTTTTTT
1 -TTTTCTT
*
2751391 CTCTTTTTT
1 -T-TTTCTT
2751400 TTTTCTT
1 TTTTCTT
2751407 TTTTCTT
1 TTTTCTT
2751414 TTTTCTT
1 TTTTCTT
2751421 TTTTCTT
1 TTTTCTT
2751428 TTTTCTT
1 TTTTCTT
2751435 TTTTCTT
1 TTTTCTT
2751442 TTTTCTT
1 TTTTCTT
2751449 TTTTCTT
1 TTTTCTT
2751456 TTTTCTT
1 TTTTCTT
*
2751463 TTTTCCT
1 TTTTCTT
*
2751470 TTTTCAT
1 TTTTCTT
*
2751477 TTTTCAT
1 TTTTCTT
2751484 TTTTCTT
1 TTTTCTT
2751491 TTCTTCT
1 TT-TTCT
2751498 CTTCAATGCA
Statistics
Matches: 158, Mismatches: 7, Indels: 19
0.86 0.04 0.10
Matches are distributed among these distances:
6 7 0.04
7 107 0.68
8 21 0.13
9 23 0.15
ACGTcount: A:0.02, C:0.15, G:0.01, T:0.82
Consensus pattern (7 bp):
TTTTCTT
Found at i:2751480 original size:1 final size:1
Alignment explanation
Indices: 2751316--2751466 Score: 86
Period size: 1 Copynumber: 151.0 Consensus size: 1
2751306 CAAAAAAATC
* * * * * * * * * * * *
2751316 TTTTCTTTTATTTTTCTTTCTTTTCTTTCTTTTCTTTCTTTTCTTCTTTTGTTTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * * * *
2751381 TTATTTTTTTCTCTTTTTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
2751446 CTTTTTTCTTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTT
2751467 CCTTTTTCAT
Statistics
Matches: 102, Mismatches: 48, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
1 102 1.00
ACGTcount: A:0.01, C:0.14, G:0.01, T:0.84
Consensus pattern (1 bp):
T
Found at i:2753522 original size:40 final size:40
Alignment explanation
Indices: 2753464--2753584 Score: 206
Period size: 40 Copynumber: 3.0 Consensus size: 40
2753454 ACCGTAGTGC
*
2753464 TACACATAAGGTCGTGCCCACCATATAGACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
2753504 TACACATAAGGTCATGCCCACCATATACACCGAATTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
2753544 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2753584 T
1 T
2753585 TTAAACCTGT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 75 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:2759938 original size:11 final size:11
Alignment explanation
Indices: 2759875--2759932 Score: 50
Period size: 11 Copynumber: 5.3 Consensus size: 11
2759865 ACAATAATGA
2759875 AAAAATAAAAT
1 AAAAATAAAAT
2759886 -AAAATAAAA-
1 AAAAATAAAAT
*
2759895 AACAGA-AAAAT
1 AA-AAATAAAAT
*
2759906 AACTACATAAAAT
1 AA--AAATAAAAT
2759919 AAAAATAAAAT
1 AAAAATAAAAT
2759930 AAA
1 AAA
2759933 CCTAAATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
10 14 0.37
11 15 0.39
12 2 0.05
13 7 0.18
ACGTcount: A:0.78, C:0.05, G:0.02, T:0.16
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:2761384 original size:13 final size:12
Alignment explanation
Indices: 2761341--2761396 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 12
2761331 GTCCGATTTA
2761341 GTTTGGGTCT-G
1 GTTTGGGTCTGG
2761352 GTTTGGGT-TGG
1 GTTTGGGTCTGG
2761363 AATGTTTGGGTACTGG
1 ---GTTTGGGT-CTGG
*
2761379 GTTTGGGTTTGG
1 GTTTGGGTCTGG
2761391 GTTTGG
1 GTTTGG
2761397 TTTGTAATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
10 1 0.03
11 9 0.24
12 9 0.24
13 8 0.21
14 8 0.21
16 3 0.08
ACGTcount: A:0.05, C:0.04, G:0.46, T:0.45
Consensus pattern (12 bp):
GTTTGGGTCTGG
Found at i:2761394 original size:25 final size:23
Alignment explanation
Indices: 2761340--2761396 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 23
2761330 GGTCCGATTT
2761340 AGTTTGGGTCTGGTTTGGGTTGG
1 AGTTTGGGTCTGGTTTGGGTTGG
2761363 AATGTTTGGGTACTGGGTTTGGGTTTGG
1 -A-GTTTGGGT-CT-GGTTTGGG-TTGG
2761391 -GTTTGG
1 AGTTTGG
2761397 TTTGTAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
24 1 0.03
25 14 0.48
26 2 0.07
27 8 0.28
28 4 0.14
ACGTcount: A:0.07, C:0.04, G:0.46, T:0.44
Consensus pattern (23 bp):
AGTTTGGGTCTGGTTTGGGTTGG
Found at i:2761409 original size:3 final size:3
Alignment explanation
Indices: 2761401--2761459 Score: 109
Period size: 3 Copynumber: 19.7 Consensus size: 3
2761391 GTTTGGTTTG
2761401 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2761449 TAA TAA AAA TA
1 TAA TAA TAA TA
2761460 GAGGTTGAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:2762633 original size:32 final size:32
Alignment explanation
Indices: 2762597--2762669 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 32
2762587 ATTTTTATTT
* * *
2762597 TTAATTTTTTTAATTATGTGTAATTTAAAATG
1 TTAATTTTTTCAATTATGTATAATTTAAAATA
* * * *
2762629 TTAATCTTTTCACTTTTTTATAATTTAAAATA
1 TTAATTTTTTCAATTATGTATAATTTAAAATA
2762661 TTAATTTTT
1 TTAATTTTT
2762670 GAATATTTTC
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (32 bp):
TTAATTTTTTCAATTATGTATAATTTAAAATA
Found at i:2764365 original size:4 final size:4
Alignment explanation
Indices: 2764356--2764437 Score: 73
Period size: 4 Copynumber: 21.2 Consensus size: 4
2764346 CGGTTGTAAG
* * *
2764356 AAGA AAGA AAGA GAG- AAGA AAGA AAGA GAG- AAGA AAGA AAGA GAG-
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
* * *
2764401 AAGA AAGA AAGG GAG- AAGA AAGA AAGGA AAGG AAGA A
1 AAGA AAGA AAGA AAGA AAGA AAGA AA-GA AAGA AAGA A
2764438 GAAGAAGGGC
Statistics
Matches: 62, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
3 8 0.13
4 50 0.81
5 4 0.06
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:2764374 original size:11 final size:11
Alignment explanation
Indices: 2764360--2764408 Score: 59
Period size: 11 Copynumber: 4.7 Consensus size: 11
2764350 TGTAAGAAGA
2764360 AAGAAAGAGAG
1 AAGAAAGAGAG
*
2764371 AAGAAAGAAAG
1 AAGAAAGAGAG
*
2764382 -AGAGA-AGA-
1 AAGAAAGAGAG
2764390 AAGAAAGAGAG
1 AAGAAAGAGAG
2764401 AAGAAAGA
1 AAGAAAGA
2764409 AAGGGAGAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
9 6 0.19
10 7 0.23
11 18 0.58
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (11 bp):
AAGAAAGAGAG
Found at i:2764427 original size:15 final size:15
Alignment explanation
Indices: 2764354--2764426 Score: 137
Period size: 15 Copynumber: 4.9 Consensus size: 15
2764344 TTCGGTTGTA
2764354 AGAAGAAAGAAAGAG
1 AGAAGAAAGAAAGAG
2764369 AGAAGAAAGAAAGAG
1 AGAAGAAAGAAAGAG
2764384 AGAAGAAAGAAAGAG
1 AGAAGAAAGAAAGAG
*
2764399 AGAAGAAAGAAAGGG
1 AGAAGAAAGAAAGAG
2764414 AGAAGAAAGAAAG
1 AGAAGAAAGAAAG
2764427 GAAAGGAAGA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
15 57 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (15 bp):
AGAAGAAAGAAAGAG
Found at i:2764442 original size:19 final size:17
Alignment explanation
Indices: 2764353--2764443 Score: 104
Period size: 15 Copynumber: 5.5 Consensus size: 17
2764343 GTTCGGTTGT
2764353 AAGAAGAAAGAAA-GAG
1 AAGAAGAAAGAAAGGAG
2764369 -AGAAGAAAGAAA-GAG
1 AAGAAGAAAGAAAGGAG
2764384 -AGAAGAAAGAAA-GAG
1 AAGAAGAAAGAAAGGAG
2764399 -AGAAGAAAGAAAGGGAG
1 AAGAAGAAAGAAA-GGAG
2764416 AAGAAAGAAAGGAAAGGAAG
1 AAG-AAGAAA-GAAAGG-AG
2764436 AAGAAGAA
1 AAGAAGAA
2764444 GGGCCCGTAA
Statistics
Matches: 69, Mismatches: 0, Indels: 9
0.88 0.00 0.12
Matches are distributed among these distances:
15 42 0.61
17 3 0.04
18 2 0.03
19 13 0.19
20 9 0.13
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (17 bp):
AAGAAGAAAGAAAGGAG
Found at i:2766069 original size:16 final size:16
Alignment explanation
Indices: 2766048--2766079 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2766038 TTGATATTTA
2766048 ATGATTTAATAATGAT
1 ATGATTTAATAATGAT
*
2766064 ATGATTTAGTAATGAT
1 ATGATTTAATAATGAT
2766080 TACTAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.44
Consensus pattern (16 bp):
ATGATTTAATAATGAT
Found at i:2766335 original size:15 final size:16
Alignment explanation
Indices: 2766286--2766345 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 16
2766276 CTAATATAAA
2766286 TTAAACAAAATATTTTT
1 TTAAACAAAATA-TTTT
2766303 TTAAACAACAATAAATATTT
1 TTAAACAA-AAT--AT-TTT
2766323 TTAAACAAAATATTTT
1 TTAAACAAAATATTTT
2766339 TTAAACA
1 TTAAACA
2766346 GGAATAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
16 10 0.26
17 10 0.26
18 3 0.08
19 4 0.10
20 12 0.31
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (16 bp):
TTAAACAAAATATTTT
Found at i:2766774 original size:54 final size:58
Alignment explanation
Indices: 2766710--2766818 Score: 147
Period size: 54 Copynumber: 1.9 Consensus size: 58
2766700 GTTTAAACAC
2766710 ACTAACAAACTAATTAAAT-ATTTTTT-T-TACATAT-A-ATATAACTTAAACTAAGAA
1 ACTAACAAACTAATTAAATAATTTTTTATATA-ATATAATATATAACTTAAACTAAGAA
* * *
2766764 ACTAAGAAACTACTTAACTAATTTTTTATATAATATAATATATAACTTAAACTAA
1 ACTAACAAACTAATTAAATAATTTTTTATATAATATAATATATAACTTAAACTAA
2766819 CATACTAATA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
54 16 0.34
55 7 0.15
56 5 0.11
57 3 0.06
58 16 0.34
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.38
Consensus pattern (58 bp):
ACTAACAAACTAATTAAATAATTTTTTATATAATATAATATATAACTTAAACTAAGAA
Found at i:2766826 original size:58 final size:54
Alignment explanation
Indices: 2766705--2766826 Score: 138
Period size: 58 Copynumber: 2.2 Consensus size: 54
2766695 TATACGTTTA
*
2766705 AACACACTAACAAACTAATTAAATATTTTTTTTACATATAATATAACTTAAACT
1 AACAAACTAACAAACTAATTAAATATTTTTTTTACATATAATATAACTTAAACT
* * * *
2766759 AAGAAACTAAGAAACTACTTAACTAATTTTTTATATA-ATATAATATATAACTTAAACT
1 AACAAACTAACAAACTAATTAAAT-ATTTTTT-T-TACATAT-A-ATATAACTTAAACT
*
2766817 AACATACTAA
1 AACAAACTAA
2766827 TATAATATAA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
54 19 0.34
55 7 0.12
56 5 0.09
57 3 0.05
58 22 0.39
ACGTcount: A:0.50, C:0.13, G:0.02, T:0.35
Consensus pattern (54 bp):
AACAAACTAACAAACTAATTAAATATTTTTTTTACATATAATATAACTTAAACT
Found at i:2766834 original size:28 final size:30
Alignment explanation
Indices: 2766794--2766856 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
2766784 ATTTTTTATA
*
2766794 TAATATAATATATAACTTAAACTAACATAC
1 TAATATAATATATAACTTAAACTAACAAAC
2766824 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
2766852 TAATA
1 TAATA
2766857 ATTTAAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.32
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:2766862 original size:21 final size:21
Alignment explanation
Indices: 2766833--2766875 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2766823 CTAATATAAT
2766833 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
2766854 ATAATTTAAATTAACAAACTA
1 ATAACTTAAACTAACAAACTA
2766875 A
1 A
2766876 CAAACTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:2766912 original size:14 final size:14
Alignment explanation
Indices: 2766893--2766954 Score: 63
Period size: 14 Copynumber: 4.3 Consensus size: 14
2766883 TTACTCGATA
2766893 TCTTCTTCTCCCTT
1 TCTTCTTCTCCCTT
*
2766907 TCTTCTTCTTCCTT
1 TCTTCTTCTCCCTT
*
2766921 TCTT-TTCTCTTTCTT
1 TCTTCTTCTC--CCTT
*
2766936 TCTTTCTTCTCCATT
1 TC-TTCTTCTCCCTT
2766951 TCTT
1 TCTT
2766955 TTTTATTAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
13 4 0.10
14 19 0.49
15 9 0.23
16 2 0.05
17 5 0.13
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.65
Consensus pattern (14 bp):
TCTTCTTCTCCCTT
Found at i:2766952 original size:19 final size:19
Alignment explanation
Indices: 2766912--2766955 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
2766902 CCCTTTCTTC
* *
2766912 TTCTTCCTTTCTTTTCTCT
1 TTCTTTCTTTCTTCTCTCT
2766931 TTCTTTCTTTCTTCTC-CAT
1 TTCTTTCTTTCTTCTCTC-T
2766950 TTCTTT
1 TTCTTT
2766956 TTTATTAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 1 0.05
19 21 0.95
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (19 bp):
TTCTTTCTTTCTTCTCTCT
Found at i:2776275 original size:9 final size:9
Alignment explanation
Indices: 2776255--2776290 Score: 63
Period size: 9 Copynumber: 3.9 Consensus size: 9
2776245 ACTTCGTCTG
2776255 AAGAATAAAA
1 AAGAA-AAAA
2776265 AAGAAAAAA
1 AAGAAAAAA
2776274 AAGAAAAAA
1 AAGAAAAAA
2776283 AAGAAAAA
1 AAGAAAAA
2776291 TGAAAAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 21 0.81
10 5 0.19
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:2776280 original size:6 final size:6
Alignment explanation
Indices: 2776262--2776309 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
2776252 CTGAAGAATA
* *
2776262 AAAAAG AAAAA- AAAGAAA AAAAAG AAAAATG AAAAAG AAAATG AAAAA
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAA-G AAAAAG AAAAAG AAAAA
2776310 AAGTGGAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
5 3 0.08
6 24 0.67
7 9 0.25
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:2776310 original size:13 final size:14
Alignment explanation
Indices: 2776279--2776310 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2776269 AAAAAAAGAA
2776279 AAAAAAGAAAAATG
1 AAAAAAGAAAAATG
2776293 -AAAAAG-AAAATG
1 AAAAAAGAAAAATG
2776305 AAAAAA
1 AAAAAA
2776311 AGTGGAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.06
Consensus pattern (14 bp):
AAAAAAGAAAAATG
Found at i:2778185 original size:45 final size:45
Alignment explanation
Indices: 2778135--2778593 Score: 769
Period size: 45 Copynumber: 10.2 Consensus size: 45
2778125 ATTTATCCCA
* * *
2778135 TAAGCTTATTTTACCAATATACTTACCATTTGTACCATAAGCTCG
1 TAAGCTTATTTTACCAATAAACTTACCATTTATTCCATAAGCTCG
* *
2778180 TAAGCTTATTTTACCAATATACTTACCATTTATTCCATAAGCGCG
1 TAAGCTTATTTTACCAATAAACTTACCATTTATTCCATAAGCTCG
2778225 TAAGCTTATTTTACCAATAAACTTACCATTTATTCCATAAGCTCG
1 TAAGCTTATTTTACCAATAAACTTACCATTTATTCCATAAGCTCG
* * * *
2778270 TAAGTTTATTTTACCAATAAACTTACCATTTCTTCTATAAGC-CA
1 TAAGCTTATTTTACCAATAAACTTACCATTTATTCCATAAGCTCG
* *
2778314 TAAGCTTATTTTACCAATATACTTACCATTTGTTCCATAAGCTCG
1 TAAGCTTATTTTACCAATAAACTTACCATTTATTCCATAAGCTCG
*
2778359 TAATCTTATTTTACCAATAAACTTACCATTTATTCCATAAGCTCG
1 TAAGCTTATTTTACCAATAAACTTACCATTTATTCCATAAGCTCG
*
2778404 TAAGCTTATTTTACCAATAAACTTGCCATTTATTCCATAAGCTCG
1 TAAGCTTATTTTACCAATAAACTTACCATTTATTCCATAAGCTCG
2778449 TAAGCTTATTTTACCAATAAACTTACCATTTATTCCATAAGCTCG
1 TAAGCTTATTTTACCAATAAACTTACCATTTATTCCATAAGCTCG
2778494 TAAGCTTATTTTACCAATAAACTTACCATTTATTCCATAAGCTCG
1 TAAGCTTATTTTACCAATAAACTTACCATTTATTCCATAAGCTCG
* *
2778539 TAAGCTTATTTTACCAATATACTTGCCA-TTATTCCATAAGCTCG
1 TAAGCTTATTTTACCAATAAACTTACCATTTATTCCATAAGCTCG
2778583 TAAGCTTATTT
1 TAAGCTTATTT
2778594 GCATACTTAC
Statistics
Matches: 391, Mismatches: 22, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
44 66 0.17
45 325 0.83
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (45 bp):
TAAGCTTATTTTACCAATAAACTTACCATTTATTCCATAAGCTCG
Found at i:2778413 original size:21 final size:21
Alignment explanation
Indices: 2778388--2778458 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
2778378 AACTTACCAT
2778388 TTATTCCATAAGCTCGTAAGC
1 TTATTCCATAAGCTCGTAAGC
* * ** *
2778409 TTATTTTACCAATAAACTTGCCA-T
1 TTA--TT-CC-ATAAGCTCGTAAGC
2778433 TTATTCCATAAGCTCGTAAGC
1 TTATTCCATAAGCTCGTAAGC
2778454 TTATT
1 TTATT
2778459 TTACCAATAA
Statistics
Matches: 35, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
20 8 0.23
21 10 0.29
22 2 0.06
23 2 0.06
24 5 0.14
25 8 0.23
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (21 bp):
TTATTCCATAAGCTCGTAAGC
Found at i:2778435 original size:179 final size:179
Alignment explanation
Indices: 2778132--2778593 Score: 800
Period size: 179 Copynumber: 2.6 Consensus size: 179
2778122 ACCATTTATC
*
2778132 CCATAAGCTTATTTTACCAATATACTTACCATTTGTACCATAAGCTCGTAAGCTTATTTTACCAA
1 CCATAAGCTTATTTTACCAATATACTTACCATTTGTTCCATAAGCTCGTAAGCTTATTTTACCAA
*
2778197 TATACTTACCATTTATTCCATAAGCGCGTAAGCTTATTTTACCAATAAACTTACCATTTATTCCA
66 TATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATAAACTTACCATTTATTCCA
* * *
2778262 TAAGCTCGTAAGTTTATTTTACCAATAAACTTACCATTTCTTCTATAAG
131 TAAGCTCGTAAGCTTATTTTACCAATAAACTTACCATTTATTCCATAAG
*
2778311 CCATAAGCTTATTTTACCAATATACTTACCATTTGTTCCATAAGCTCGTAATCTTATTTTACCAA
1 CCATAAGCTTATTTTACCAATATACTTACCATTTGTTCCATAAGCTCGTAAGCTTATTTTACCAA
* *
2778376 TAAACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATAAACTTGCCATTTATTCCA
66 TATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATAAACTTACCATTTATTCCA
2778441 TAAGCTCGTAAGCTTATTTTACCAATAAACTTACCATTTATTCCATAAG
131 TAAGCTCGTAAGCTTATTTTACCAATAAACTTACCATTTATTCCATAAG
* * *
2778490 CTCGTAAGCTTATTTTACCAATAAACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCA
1 C-CATAAGCTTATTTTACCAATATACTTACCATTTGTTCCATAAGCTCGTAAGCTTATTTTACCA
*
2778555 ATATACTTGCCA-TTATTCCATAAGCTCGTAAGCTTATTT
65 ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
2778594 GCATACTTAC
Statistics
Matches: 268, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
179 199 0.74
180 69 0.26
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (179 bp):
CCATAAGCTTATTTTACCAATATACTTACCATTTGTTCCATAAGCTCGTAAGCTTATTTTACCAA
TATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATAAACTTACCATTTATTCCA
TAAGCTCGTAAGCTTATTTTACCAATAAACTTACCATTTATTCCATAAG
Found at i:2778481 original size:24 final size:24
Alignment explanation
Indices: 2778454--2778527 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
2778444 GCTCGTAAGC
2778454 TTATTTTACCAATAAACTTACCAT
1 TTATTTTACCAATAAACTTACCAT
* *
2778478 TTA--TT-CC-ATAAGCTCGTA--AGC
1 TTATTTTACCAATAAACT--TACCA-T
2778499 TTATTTTACCAATAAACTTACCAT
1 TTATTTTACCAATAAACTTACCAT
2778523 TTATT
1 TTATT
2778528 CCATAAGCTC
Statistics
Matches: 37, Mismatches: 4, Indels: 18
0.63 0.07 0.31
Matches are distributed among these distances:
20 7 0.19
21 5 0.14
22 4 0.11
23 4 0.11
24 10 0.27
25 7 0.19
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.42
Consensus pattern (24 bp):
TTATTTTACCAATAAACTTACCAT
Found at i:2778488 original size:20 final size:20
Alignment explanation
Indices: 2778465--2778533 Score: 50
Period size: 20 Copynumber: 3.2 Consensus size: 20
2778455 TATTTTACCA
2778465 ATAAACTTACCATTTATTCC
1 ATAAACTTACCATTTATTCC
* * *
2778485 ATAAGCTCGTAAGCTTATTT-TACC
1 ATAAACT--T-A-C-CATTTATTCC
2778509 AATAAACTTACCATTTATTCC
1 -ATAAACTTACCATTTATTCC
2778530 ATAA
1 ATAA
2778534 GCTCGTAAGC
Statistics
Matches: 36, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
20 14 0.39
21 4 0.11
22 2 0.06
23 2 0.06
24 4 0.11
25 10 0.28
ACGTcount: A:0.36, C:0.22, G:0.04, T:0.38
Consensus pattern (20 bp):
ATAAACTTACCATTTATTCC
Found at i:2778824 original size:61 final size:60
Alignment explanation
Indices: 2778703--2778824 Score: 138
Period size: 61 Copynumber: 2.0 Consensus size: 60
2778693 GTAGTCTTAA
* * *
2778703 ACCTACACTAAGCTAATGCCATAGTGCTAATCCGGATAATACACGTAAGGTCGTGCCCACC
1 ACCTACACTAAGCTAACGCCATAGTGCTAATCCGGATAATACAC-TAAGGTCATACCCACC
* * * * *
2778764 ACCTACACTAAGCTTACGCTATAGTGCTAATTCGGACATGATACA-TAAGGTCATATCCACC
1 ACCTACACTAAGCTAACGCCATAGTGCTAATCCGG--ATAATACACTAAGGTCATACCCACC
2778825 TTTCCTGCAC
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
61 44 0.86
63 7 0.14
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (60 bp):
ACCTACACTAAGCTAACGCCATAGTGCTAATCCGGATAATACACTAAGGTCATACCCACC
Found at i:2783701 original size:267 final size:266
Alignment explanation
Indices: 2783124--2783786 Score: 848
Period size: 267 Copynumber: 2.5 Consensus size: 266
2783114 TTCCCTAAAG
* * * * *
2783124 AACAGTGGAATGAATCAACATCCCCAGATCTTATTTTCCCTCAAGAAAAAGTGGAACAAACCCTC
1 AACAGTGGAATGAATCAACATCCCCAGATCTAATTTTCCCTCAAGAAGAAGCGAAACAATCCCTC
* * *
2783189 TCTTTCAAGATTTGATCTTCCCTAAGTAACAGTGGAACAAGTCTACCTCAATTCAACATTT-CC-
66 TCTTTCAAGATTTGATCTTCCCTGAGTAACAGTGGAACAAGTCTACCTCGATTCAA-TTTTCCCT
* ** * *
2783252 TGAAAAATAGTGGAATAAATCAACATTTCCAAATCTGATTTTCCCTCAAGAAGAAGCGAAACAGA
130 TG-AAAACAGTGGAATAAATCAACATCCCCAAATCTGATTTTACCTCAAGAAGAAGCGAAACAAA
* * *
2783317 TCCCTCTCTTTCAAGATTTAACTTCCCTAAGTAACAGTGGAATAAGTCTTCCTCGGTTCAATCCT
194 TCCCTCTCTTTCAAGATTTAACTTCCCTAAGTAACAGTAGAATAAGTCTGCCTCGATTCAATCCT
*
2783382 CCTAGAGT
259 CCTAGAGC
* *** *
2783390 AACAGTGGAATGAATCAACTTGTGCAGATCTAATTTTACCTCAAGAAGAAGCGAAACAGATCCCT
1 AACAGTGGAATGAATCAACATCCCCAGATCTAATTTTCCCTCAAGAAGAAGCGAAACA-ATCCCT
* * * *
2783455 CTCTTTCAAGATTTGATCTTCCCTGAGTAACAATGGAAGAAGTCTGCGTCGATTCAATTTTCCCT
65 CTCTTTCAAGATTTGATCTTCCCTGAGTAACAGTGGAACAAGTCTACCTCGATTCAATTTTCCCT
* ** * *
2783520 TG-TAACAGTGGAATGGATCAACATCCCCAGATCTTATTTTACCTCAAGAAGAAGC-AGAACAAA
130 TGAAAACAGTGGAATAAATCAACATCCCCAAATCTGATTTTACCTCAAGAAGAAGCGA-AACAAA
* * *
2783583 TCCCTCTCTTTCAAGATTTGATCTTTCCTAAGTAACAGTAGAATAAGTCTGCCTCGATTCAATCT
194 TCCCTCTCTTTCAAGATTT-AACTTCCCTAAGTAACAGTAGAATAAGTCTGCCTCGATTCAATCC
*
2783648 TCCTTGAGC
258 TCCTAGAGC
* * * * *
2783657 AACAGTGGAATGAATTAACGTCCCCATATCTGATTTTCCCTCAAGAAGAAACGAAACATATCCCT
1 AACAGTGGAATGAATCAACATCCCCAGATCTAATTTTCCCTCAAGAAGAAGCGAAACA-ATCCCT
* * * *
2783722 CTCTTTCAAGATTTGATATTCCTTGAGTAATAGTGGAACAAGTCTACCTCGATTCAATATTCCCT
65 CTCTTTCAAGATTTGATCTTCCCTGAGTAACAGTGGAACAAGTCTACCTCGATTCAATTTTCCCT
2783787 GAAGAAAAAC
Statistics
Matches: 339, Mismatches: 53, Indels: 9
0.85 0.13 0.02
Matches are distributed among these distances:
265 1 0.00
266 120 0.35
267 216 0.64
268 2 0.01
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (266 bp):
AACAGTGGAATGAATCAACATCCCCAGATCTAATTTTCCCTCAAGAAGAAGCGAAACAATCCCTC
TCTTTCAAGATTTGATCTTCCCTGAGTAACAGTGGAACAAGTCTACCTCGATTCAATTTTCCCTT
GAAAACAGTGGAATAAATCAACATCCCCAAATCTGATTTTACCTCAAGAAGAAGCGAAACAAATC
CCTCTCTTTCAAGATTTAACTTCCCTAAGTAACAGTAGAATAAGTCTGCCTCGATTCAATCCTCC
TAGAGC
Found at i:2783731 original size:134 final size:134
Alignment explanation
Indices: 2783124--2783784 Score: 787
Period size: 133 Copynumber: 5.0 Consensus size: 134
2783114 TTCCCTAAAG
* * * * *
2783124 AACAGTGGAATGAATCAACATCCCCAGATCTTATTTTCCCTCAAGAAAAAGTGGAACA-AACCCT
1 AACAGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAAGAAGAAGCGAAACAGATCCCT
*
2783188 CTCTTTCAAGATTTGATCTTCCCTAAGTAACAGTGGAACAAGTCTACCTCAATTCAA-CATTTCC
66 CTCTTTCAAGATTTGATCTTCCCTAAGTAACAGTGGAACAAGTCTACCTCGATTCAATC--TTCC
**
2783252 -TGAAA
129 TTGAGT
* * ** *
2783257 AATAGTGGAATAAATCAACATTTCCAAATCTGATTTTCCCTCAAGAAGAAGCGAAACAGATCCCT
1 AACAGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAAGAAGAAGCGAAACAGATCCCT
* * * * * *
2783322 CTCTTTCAAGATTT-AACTTCCCTAAGTAACAGTGGAATAAGTCTTCCTCGGTTCAATCCTCCTA
66 CTCTTTCAAGATTTGATCTTCCCTAAGTAACAGTGGAACAAGTCTACCTCGATTCAATCTTCCTT
2783386 GAGT
131 GAGT
* *** * *
2783390 AACAGTGGAATGAATCAACTTGTGCAGATCTAATTTTACCTCAAGAAGAAGCGAAACAGATCCCT
1 AACAGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAAGAAGAAGCGAAACAGATCCCT
* * * * * *
2783455 CTCTTTCAAGATTTGATCTTCCCTGAGTAACAATGGAAGAAGTCTGCGTCGATTCAATTTTCCCT
66 CTCTTTCAAGATTTGATCTTCCCTAAGTAACAGTGGAACAAGTCTACCTCGATTCAATCTT-CCT
2783520 T--GT
130 TGAGT
* * * *
2783523 AACAGTGGAATGGATCAACATCCCCAGATCTTATTTTACCTCAAGAAGAAGC-AGAACAAATCCC
1 AACAGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAAGAAGAAGCGA-AACAGATCCC
* * * *
2783587 TCTCTTTCAAGATTTGATCTTTCCTAAGTAACAGTAGAATAAGTCTGCCTCGATTCAATCTTCCT
65 TCTCTTTCAAGATTTGATCTTCCCTAAGTAACAGTGGAACAAGTCTACCTCGATTCAATCTTCCT
*
2783652 TGAGC
130 TGAGT
* * * * *
2783657 AACAGTGGAATGAATTAACGTCCCCATATCTGATTTTCCCTCAAGAAGAAACGAAACATATCCCT
1 AACAGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAAGAAGAAGCGAAACAGATCCCT
* * * * *
2783722 CTCTTTCAAGATTTGATATTCCTTGAGTAATAGTGGAACAAGTCTACCTCGATTCAATATTCC
66 CTCTTTCAAGATTTGATCTTCCCTAAGTAACAGTGGAACAAGTCTACCTCGATTCAATCTTCC
2783785 CTGAAGAAAA
Statistics
Matches: 450, Mismatches: 69, Indels: 17
0.84 0.13 0.03
Matches are distributed among these distances:
132 8 0.02
133 271 0.60
134 167 0.37
135 4 0.01
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (134 bp):
AACAGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAAGAAGAAGCGAAACAGATCCCT
CTCTTTCAAGATTTGATCTTCCCTAAGTAACAGTGGAACAAGTCTACCTCGATTCAATCTTCCTT
GAGT
Found at i:2784014 original size:3 final size:3
Alignment explanation
Indices: 2783983--2784062 Score: 101
Period size: 3 Copynumber: 27.0 Consensus size: 3
2783973 TCCGGCTATA
* * * *
2783983 ATT A-T ATT ACTT ATT AAT ATT AAT ATT ATT ATT AAT ATT ATT AAT
1 ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2784028 ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2784063 TATTTCTGTA
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
2 4 0.06
3 59 0.89
4 3 0.05
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:2785508 original size:28 final size:28
Alignment explanation
Indices: 2785449--2785517 Score: 88
Period size: 29 Copynumber: 2.5 Consensus size: 28
2785439 GAATCTGTAT
2785449 TTTTATTTATTTTAATTTGTCCATGCAA
1 TTTTATTTATTTTAATTTGTCCATGCAA
**
2785477 TTTTATTTTATTTTAATTTAGTCC-T-CGG
1 TTTTA-TTTATTTTAATTT-GTCCATGCAA
2785505 TTTTATTTATTTT
1 TTTTATTTATTTT
2785518 TATTCTTTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
27 8 0.22
28 11 0.30
29 14 0.38
30 4 0.11
ACGTcount: A:0.20, C:0.09, G:0.07, T:0.64
Consensus pattern (28 bp):
TTTTATTTATTTTAATTTGTCCATGCAA
Found at i:2785518 original size:28 final size:29
Alignment explanation
Indices: 2785449--2785519 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 29
2785439 GAATCTGTAT
2785449 TTTTATTTA-TTTTAATTTGTCCATGCAA
1 TTTTATTTATTTTTAATTTGTCCATGCAA
**
2785477 TTTTATTT-TATTTTAATTTAGTCC-T-CGG
1 TTTTATTTAT-TTTTAATTT-GTCCATGCAA
2785505 TTTTATTTATTTTTA
1 TTTTATTTATTTTTA
2785520 TTCTTTGTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
28 22 0.59
29 11 0.30
30 4 0.11
ACGTcount: A:0.21, C:0.08, G:0.07, T:0.63
Consensus pattern (29 bp):
TTTTATTTATTTTTAATTTGTCCATGCAA
Found at i:2788829 original size:65 final size:65
Alignment explanation
Indices: 2788760--2788881 Score: 174
Period size: 65 Copynumber: 1.9 Consensus size: 65
2788750 ATTGCATTCA
* *
2788760 ATGTTTCAAAATAGCCAGGAGTGCACCGATGCATGG-TATGTGCATCGGTACACAAAATCAATTT
1 ATGTTTCAAAATAGCCAAGAGTGCACCGATACATGGCT-TGTGCATCGGTACACAAAATCAATTT
2788824 G
65 G
* ** *
2788825 ATGTTTCAAATTATTCAAGAGTGCATCGATACATGGCTTGTGCATCGGTACACAAAA
1 ATGTTTCAAAATAGCCAAGAGTGCACCGATACATGGCTTGTGCATCGGTACACAAAA
2788882 CACATTCGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
65 49 0.98
66 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (65 bp):
ATGTTTCAAAATAGCCAAGAGTGCACCGATACATGGCTTGTGCATCGGTACACAAAATCAATTTG
Found at i:2791621 original size:23 final size:22
Alignment explanation
Indices: 2791548--2791627 Score: 74
Period size: 23 Copynumber: 3.6 Consensus size: 22
2791538 CATGGCAGAG
*
2791548 TGCATCAATGCACATTCAAGGA
1 TGCATCGATGCACATTCAAGGA
* * *
2791570 GTGCATAGGTGCATC-TTC-ATGA
1 -TGCATCGATGCA-CATTCAAGGA
*
2791592 TGTATCGATGCACATTCAAGGGA
1 TGCATCGATGCACATTCAA-GGA
2791615 TGCATCGATGCAC
1 TGCATCGATGCAC
2791628 TGACTAGTGT
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
20 1 0.02
21 12 0.27
22 4 0.09
23 26 0.59
24 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:2796208 original size:21 final size:22
Alignment explanation
Indices: 2796184--2796224 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2796174 AGAGACAAAC
2796184 AAATAATTAGAAGAA-AAATAG
1 AAATAATTAGAAGAATAAATAG
*
2796205 AAATAATTGGAAGAATAAAT
1 AAATAATTAGAAGAATAAAT
2796225 TAGGGTTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.63, C:0.00, G:0.15, T:0.22
Consensus pattern (22 bp):
AAATAATTAGAAGAATAAATAG
Found at i:2802784 original size:25 final size:25
Alignment explanation
Indices: 2802721--2802817 Score: 83
Period size: 25 Copynumber: 3.8 Consensus size: 25
2802711 TTCGCTTCAA
* *
2802721 GAAAGAAATAAAAATGAAAATAAAT
1 GAAAGAAAGAAAAAAGAAAATAAAT
* *
2802746 -ATAA-ATATAAAAAAGGAAAAATAAAT
1 GA-AAGAAAGAAAAAA-G-AAAATAAAT
*
2802772 GAAAGAAAGAAAAAAGAAAATGAAT
1 GAAAGAAAGAAAAAAGAAAATAAAT
*
2802797 GAAAGAAAAGAAGAAA-AAAAT
1 GAAAG-AAAGAAAAAAGAAAAT
2802818 TAAAAAAAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
24 9 0.15
25 21 0.35
26 21 0.35
27 9 0.15
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.12
Consensus pattern (25 bp):
GAAAGAAAGAAAAAAGAAAATAAAT
Found at i:2802792 original size:21 final size:22
Alignment explanation
Indices: 2802768--2802813 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
2802758 AAGGAAAAAT
2802768 AAATGAAAGAAAGAAAA-AAGA
1 AAATGAAAGAAAGAAAAGAAGA
*
2802789 AAATGAATGAAAGAAAAGAAGA
1 AAATGAAAGAAAGAAAAGAAGA
2802811 AAA
1 AAA
2802814 AAATTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.07
Consensus pattern (22 bp):
AAATGAAAGAAAGAAAAGAAGA
Found at i:2804324 original size:135 final size:135
Alignment explanation
Indices: 2804078--2804324 Score: 354
Period size: 135 Copynumber: 1.8 Consensus size: 135
2804068 AACCAAACAT
* * *
2804078 GATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAATATCCCTATATCTAATTTTCCCTCAAGA
1 GATTCAATATTCCCTGAAGAACAATGGAATGAATCAATATCCCCATATCTAATTTTCCCTCAAGA
* * * *
2804143 AGAAGTGAAACAGATCAATTTCTTTCAAGATTTGATATTCCCTGAGTAACAGTAGATTCAAGTAT
66 AGAAGCGAAACAAATCAATCTCTTTCAAGATTTGATATTCCATGAGTAACAGTAGATTCAAGTAT
2804208 ACCTC
131 ACCTC
*
2804213 GATTCAATATTCCCT-AAGTAACAATGGAATGAATCAA-AGTCCCCATATCTGATTTTCCCTCAA
1 GATTCAATATTCCCTGAAG-AACAATGGAATGAATCAATA-TCCCCATATCTAATTTTCCCTCAA
* * **
2804276 GAAGAAGCGGATCAAATCCCTCTCTTTCAAGATTTGATATTCCATGAGT
64 GAAGAAGCGAAACAAATCAATCTCTTTCAAGATTTGATATTCCATGAGT
2804325 GACTGTGGAA
Statistics
Matches: 98, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
134 4 0.04
135 94 0.96
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (135 bp):
GATTCAATATTCCCTGAAGAACAATGGAATGAATCAATATCCCCATATCTAATTTTCCCTCAAGA
AGAAGCGAAACAAATCAATCTCTTTCAAGATTTGATATTCCATGAGTAACAGTAGATTCAAGTAT
ACCTC
Found at i:2804596 original size:6 final size:6
Alignment explanation
Indices: 2804585--2804631 Score: 58
Period size: 6 Copynumber: 7.5 Consensus size: 6
2804575 CGCCTGGCTC
* *
2804585 TTTTAT TTTTAT TTTATAT ATTTTAT TTCTAT TTCTAT TTTTAT TTT
1 TTTTAT TTTTAT TTT-TAT -TTTTAT TTTTAT TTTTAT TTTTAT TTT
2804632 ATTATAAGCC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
6 28 0.76
7 6 0.16
8 3 0.08
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:2804608 original size:20 final size:18
Alignment explanation
Indices: 2804585--2804631 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
2804575 CGCCTGGCTC
2804585 TTTTATTTTTATTTTATAT
1 TTTTATTTTTA-TTTATAT
* *
2804604 ATTTTATTTCTATTTCTAT
1 -TTTTATTTTTATTTATAT
2804623 TTTTATTTT
1 TTTTATTTT
2804632 ATTATAAGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 8 0.33
19 6 0.25
20 10 0.42
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTATTTTTATTTATAT
Found at i:2808363 original size:14 final size:14
Alignment explanation
Indices: 2808344--2808370 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2808334 TTTTTATCTA
2808344 TTAAAATTATTTTC
1 TTAAAATTATTTTC
2808358 TTAAAATTATTTT
1 TTAAAATTATTTT
2808371 AAAGGATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (14 bp):
TTAAAATTATTTTC
Found at i:2812025 original size:30 final size:30
Alignment explanation
Indices: 2811937--2812130 Score: 115
Period size: 30 Copynumber: 6.5 Consensus size: 30
2811927 AATTTACAGC
* * * *
2811937 ACTAAAACAACAAAAATAGAAACTTAAATG
1 ACTAAAATAATAAAAATAGAAAGTTAAAGG
* *
2811967 ACTAAAATAATAAAAACATAAAGTTAAAGG
1 ACTAAAATAATAAAAATAGAAAGTTAAAGG
*
2811997 ACTAAAATAGA-AAAAATAGAAAGATAAAGG
1 ACTAAAATA-ATAAAAATAGAAAGTTAAAGG
* * ** * * *
2812027 GCT-GAACCATAAATACAAAAAGTTAAAGG
1 ACTAAAATAATAAAAATAGAAAGTTAAAGG
* * ** * * * *
2812056 ACCATAATAGCAAATACAAAAATTTAAAGG
1 ACTAAAATAATAAAAATAGAAAGTTAAAGG
* * *
2812086 ACTAAAATAGTAAAAATAGACA-TTTAAGTG
1 ACTAAAATAATAAAAATAGAAAGTTAAAG-G
*
2812116 ACTAAAATCATAAAA
1 ACTAAAATAATAAAA
2812131 GCATAATCTT
Statistics
Matches: 125, Mismatches: 35, Indels: 8
0.74 0.21 0.05
Matches are distributed among these distances:
28 1 0.01
29 23 0.18
30 100 0.80
31 1 0.01
ACGTcount: A:0.60, C:0.10, G:0.11, T:0.19
Consensus pattern (30 bp):
ACTAAAATAATAAAAATAGAAAGTTAAAGG
Found at i:2813537 original size:3 final size:3
Alignment explanation
Indices: 2813529--2813588 Score: 104
Period size: 3 Copynumber: 20.0 Consensus size: 3
2813519 AATTTAAATT
2813529 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
2813575 ATA ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA
2813589 TTTTTTGTAG
Statistics
Matches: 55, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
3 50 0.91
4 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2814414 original size:69 final size:67
Alignment explanation
Indices: 2814289--2814491 Score: 254
Period size: 69 Copynumber: 3.0 Consensus size: 67
2814279 AATTTCCAAG
* *
2814289 ACTTTTGTTTCAAGAGAAAC-GACTCAAAGATGA-TTTTTCTCAAAATAAATTATCTCAAGAGAG
1 ACTTTTGTTTCAA-AGAAACAGACTCAAAGAT-ATTTTTTCTCAAAAGAAATTGTCTCAAGAGAG
2814352 ACAA
64 ACAA
* *
2814356 ACTTTTGTTTACAAAGAAACAGACTCAAAGATTTTTTTTTCTCAAAAGAAATTGTCTCAAGGGAG
1 ACTTTTGTTT-CAAAGAAACAGACTCAAAGA-TATTTTTTCTCAAAAGAAATTGTCTCAAGAGAG
2814421 AC-A
64 ACAA
* * *
2814424 ACATTTTGTTTCCAAAGAAACAAACTC-AA-ATATTTTTTCTCAAAAGAAACTGTCTTAAGAGAG
1 AC-TTTTGTTT-CAAAGAAACAGACTCAAAGATATTTTTTCTCAAAAGAAATTGTCTCAAGAGAG
2814487 ACAA
64 ACAA
2814491 A
1 A
2814492 ATTCGTTTCA
Statistics
Matches: 120, Mismatches: 10, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
66 31 0.26
67 19 0.16
68 18 0.15
69 52 0.43
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (67 bp):
ACTTTTGTTTCAAAGAAACAGACTCAAAGATATTTTTTCTCAAAAGAAATTGTCTCAAGAGAGAC
AA
Found at i:2817144 original size:2 final size:2
Alignment explanation
Indices: 2817137--2817173 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2817127 TGTGAAAAGA
2817137 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
2817174 GGTTAGAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Done.