Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001111.1 Hibiscus syriacus cultivar Beakdansim tig00002193_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: 3891333
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 17
Found at i:3043278 original size:473 final size:473
Alignment explanation
Indices: 3042494--3043456 Score: 1148
Period size: 473 Copynumber: 2.0 Consensus size: 473
3042484 GATGGCATTC
* **
3042494 TTCCTACGTGATGAGGATGTCTATCCGTCTTTAAAGATAAATTGGAGACAACATGGTTCCTACGA
1 TTCCTACGTGATGAGGACGTCTATCCGTCTTTAAAGATAAATTGGAGACAACACAGTTCCTACGA
* * * * ** * *
3042559 GATGAGGAAGTCTGGTTATCTGATGATGACGCTGCTCCTACGTGTTGAGGAGATGTGATCACTTG
66 GATGAGGAAGTCTGGTTATCTAAGGATGAAGCTACTCCTACGCATTGAGGAGATCTGATCACTGG
** * * * * * * * *
3042624 ATGATATTGTTCTTACGTGACGAGGACTTCTAGTCGTCTTTAAGGATAATTTGGAGACAACAAGG
131 ACAACATTATTCCTACGTAACGAGGACATCTAGCCATCTTTAAGGATAATTCGGAGACAACAAGG
* * *
3042689 TTCCCATATGATAAGGAAGTTCGATTTCCTAAGGATGACGTTGCTCCTACGTGTTGAGGAGATAT
196 TTCCCACATGATAAGGAAGTTCGATTTCCTAAGGATGACGCTGCTCCTACGTGTTAAGGAGATAT
* * * * * * * *
3042754 GGTCGGTGGATGACATTGTTCCTACGTTATTAGGACCTCTAGCCGTCTTTAGGGATAATTTGGAG
261 GGTCAGTGGACGACATTATTCCTACATGATGAGGACCTCTAGCCATCTTTAGGGATAACTTGGAG
* *
3042819 ACAACACAGTTCCTATGTGATGACAAAGTCTGATTGCCTA-AGGATGACGCTACTCCTACGTGTT
326 ACAACACAGTACCTACGTGATGACAAAGTCTGATTGCC-AGAGGATGACGCTACTCCTACGTGTT
* * **
3042883 GAGGATATCTAGTCGGTGGACGACATTATTCCTA-ACTGATAAGGACATCTAACC-ATCTTTCTG
390 AAGGAGATCTAGTCGGTGGACGACATTATTCCTACA-TGATAAGGACATCTAACCGA-CTTTAGG
* *
3042946 GATAATTTGGAGACAACACGG
453 GATAATTTAGAGACAACACGA
** * * *
3042967 TTCCTACGTGATGAGGACGTCTATCCGTCTTTAGGGATAATTTGGAGCCAACACAGTTCCTACGT
1 TTCCTACGTGATGAGGACGTCTATCCGTCTTTAAAGATAAATTGGAGACAACACAGTTCCTACGA
* * * *
3043032 GATGAGGAAGTCTGGTTATCTAAGGATGAAGCTACTCCTATGCATTTAGGAGATCTGGTCAGTGG
66 GATGAGGAAGTCTGGTTATCTAAGGATGAAGCTACTCCTACGCATTGAGGAGATCTGATCACTGG
* * * *
3043097 ACAACATTATTCCTATGTAATGAGGACATCTAGCCATCTTTAGGGATAATTCGGAGAGAACACA-
131 ACAACATTATTCCTACGTAACGAGGACATCTAGCCATCTTTAAGGATAATTCGGAGACAACA-AG
** * * * *
3043161 GTAT-TTACGTGATAAGGAAGTCTTG-TTAT-CTGAGGATTACGCTGCTCCTACGTGTTAAGGAG
195 GT-TCCCACATGATAAGGAAGT-TCGATT-TCCTAAGGATGACGCTGCTCCTACGTGTTAAGGAG
* **
3043223 ATATGGTCAGTGGACGACGTTATTCCTACATGATGAGGATGTCTAGCCATCTTTAGGGATAACTT
257 ATATGGTCAGTGGACGACATTATTCCTACATGATGAGGACCTCTAGCCATCTTTAGGGATAACTT
* ** * * *
3043288 GGAGACAACACGGTACCTACGTGATGAGGAAGTCTGATTTCCAGGGGATGACGCTGCTCCTACGT
322 GGAGACAACACAGTACCTACGTGATGACAAAGTCTGATTGCCAGAGGATGACGCTACTCCTACGT
* * * * *
3043353 GTTAAGGAGATCTAGTCGGTGGACGACATTGTTCGTACATTATGAGGACATCTAGCCGACTTTAG
387 GTTAAGGAGATCTAGTCGGTGGACGACATTATTCCTACATGATAAGGACATCTAACCGACTTTAG
3043418 GGATAATTTAGAGACAACACGA
452 GGATAATTTAGAGACAACACGA
*
3043440 TTCCTACATGATGAGGA
1 TTCCTACGTGATGAGGA
3043457 AGTTTGGTTA
Statistics
Matches: 409, Mismatches: 74, Indels: 14
0.82 0.15 0.03
Matches are distributed among these distances:
472 1 0.00
473 401 0.98
474 7 0.02
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (473 bp):
TTCCTACGTGATGAGGACGTCTATCCGTCTTTAAAGATAAATTGGAGACAACACAGTTCCTACGA
GATGAGGAAGTCTGGTTATCTAAGGATGAAGCTACTCCTACGCATTGAGGAGATCTGATCACTGG
ACAACATTATTCCTACGTAACGAGGACATCTAGCCATCTTTAAGGATAATTCGGAGACAACAAGG
TTCCCACATGATAAGGAAGTTCGATTTCCTAAGGATGACGCTGCTCCTACGTGTTAAGGAGATAT
GGTCAGTGGACGACATTATTCCTACATGATGAGGACCTCTAGCCATCTTTAGGGATAACTTGGAG
ACAACACAGTACCTACGTGATGACAAAGTCTGATTGCCAGAGGATGACGCTACTCCTACGTGTTA
AGGAGATCTAGTCGGTGGACGACATTATTCCTACATGATAAGGACATCTAACCGACTTTAGGGAT
AATTTAGAGACAACACGA
Found at i:3043469 original size:278 final size:278
Alignment explanation
Indices: 3042967--3043502 Score: 677
Period size: 278 Copynumber: 1.9 Consensus size: 278
3042957 GACAACACGG
* * * * * *
3042967 TTCCTACGTGATGAGGACGTCTATCCGTCTTTAGGGATAATTTGGAGCCAACACAGTTCCTACGT
1 TTCCTACATGATGAGGACGTCTAGCCATCTTTAGGGATAACTTGGAGACAACACAGTACCTACGT
* * * * *
3043032 GATGAGGAAGTCTGGTTATCTAAGGATGAAGCTACTCCTATGCATTTAGGAGATCTGGTCAGTGG
66 GATGAGGAAGTCTGATTATCCAAGGATGAAGCTACTCCTACGCATTAAGGAGATCTAGTCAGTGG
** * *
3043097 ACAACATTATTCCTATGTAATGAGGACATCTAGCCATCTTTAGGGATAATTCGGAGAGAACACAG
131 ACAACATTATTCCTACATAATGAGGACATCTAGCCATCTTTAGGGATAATTCAGAGACAACACAG
* * *
3043162 TATTTACGTGATAAGGAAGTCTTGTTATCTGAGGATTACGCTGCTCCTACGTGTTAAGGAGATAT
196 TATTTACATGATAAGGAAGTCTTGTTATCTGAGGATGACGCTGCTCCTACGCGTTAAGGAGATAT
3043227 GGTCAGTGGACGACGTTA
261 GGTCAGTGGACGACGTTA
* *
3043245 TTCCTACATGATGAGGATGTCTAGCCATCTTTAGGGATAACTTGGAGACAACACGGTACCTACGT
1 TTCCTACATGATGAGGACGTCTAGCCATCTTTAGGGATAACTTGGAGACAACACAGTACCTACGT
* * * ** *
3043310 GATGAGGAAGTCTGATT-TCCAGGGGATGACGCTGCTCCTACGTGTTAAGGAGATCTAGTCGGTG
66 GATGAGGAAGTCTGATTATCCA-AGGATGAAGCTACTCCTACGCATTAAGGAGATCTAGTCAGTG
* * * * *
3043374 GACGACATTGTTCGTACATTATGAGGACATCTAGCCGA-CTTTAGGGATAATTTAGAGACAACAC
130 GACAACATTATTCCTACATAATGAGGACATCTAGCC-ATCTTTAGGGATAATTCAGAGACAACAC
* * * *
3043438 -G-ATTCCTACATGATGAGGAAGT-TTGGTTATCTGAGGATGATGCTGCTCCTATGCGTTGAGGA
194 AGTATT--TACATGATAAGGAAGTCTT-GTTATCTGAGGATGACGCTGCTCCTACGCGTTAAGGA
3043500 GAT
256 GAT
3043503 CTATTCGATT
Statistics
Matches: 218, Mismatches: 35, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
276 3 0.01
277 6 0.03
278 208 0.95
279 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (278 bp):
TTCCTACATGATGAGGACGTCTAGCCATCTTTAGGGATAACTTGGAGACAACACAGTACCTACGT
GATGAGGAAGTCTGATTATCCAAGGATGAAGCTACTCCTACGCATTAAGGAGATCTAGTCAGTGG
ACAACATTATTCCTACATAATGAGGACATCTAGCCATCTTTAGGGATAATTCAGAGACAACACAG
TATTTACATGATAAGGAAGTCTTGTTATCTGAGGATGACGCTGCTCCTACGCGTTAAGGAGATAT
GGTCAGTGGACGACGTTA
Found at i:3043505 original size:139 final size:139
Alignment explanation
Indices: 3042967--3043505 Score: 593
Period size: 139 Copynumber: 3.9 Consensus size: 139
3042957 GACAACACGG
* * * * * *
3042967 TTCCTACGTGATGAGGACGTCTATCCGTCTTTAGGGATAATTTGGAGCCAACAC-AGTTCCTACG
1 TTCCTACATAATGAGGACATCTAGCCATCTTTAGGGATAATTTGGAGACAACACGA-TTCCTACG
* * * * * * *
3043031 TGATGAGGAAGTCTGGTTATCTAAGGATGAAGCTACTCCTATGCATTTAGGAGATCTGGTCAGTG
65 TGATGAGGAAGTCTGGTTATCTGAGGATGACGCTGCTCCTACGCGTTAAGGAGATCTAGTCAGTG
*
3043096 GACAACATTA
130 GACGACATTA
** * *
3043106 TTCCTATGTAATGAGGACATCTAGCCATCTTTAGGGATAATTCGGAGAGAACACAGTATT--TAC
1 TTCCTACATAATGAGGACATCTAGCCATCTTTAGGGATAATTTGGAGACAACAC-G-ATTCCTAC
* * * * * *
3043169 GTGATAAGGAAGTCTTGTTATCTGAGGATTACGCTGCTCCTACGTGTTAAGGAGATATGGTCAGT
64 GTGATGAGGAAGTCTGGTTATCTGAGGATGACGCTGCTCCTACGCGTTAAGGAGATCTAGTCAGT
*
3043234 GGACGACGTTA
129 GGACGACATTA
* ** * * *
3043245 TTCCTACATGATGAGGATGTCTAGCCATCTTTAGGGATAACTTGGAGACAACACGGTACCTACGT
1 TTCCTACATAATGAGGACATCTAGCCATCTTTAGGGATAATTTGGAGACAACACGATTCCTACGT
* * * * *
3043310 GATGAGGAAGTCTGATT-TCCAGGGGATGACGCTGCTCCTACGTGTTAAGGAGATCTAGTCGGTG
66 GATGAGGAAGTCTGGTTAT-CTGAGGATGACGCTGCTCCTACGCGTTAAGGAGATCTAGTCAGTG
*
3043374 GACGACATTG
130 GACGACATTA
* * * *
3043384 TTCGTACATTATGAGGACATCTAGCCGA-CTTTAGGGATAATTTAGAGACAACACGATTCCTACA
1 TTCCTACATAATGAGGACATCTAGCC-ATCTTTAGGGATAATTTGGAGACAACACGATTCCTACG
* * * *
3043448 TGATGAGGAAGTTTGGTTATCTGAGGATGATGCTGCTCCTATGCGTTGAGGAGATCTA
65 TGATGAGGAAGTCTGGTTATCTGAGGATGACGCTGCTCCTACGCGTTAAGGAGATCTA
3043506 TTCGATTACC
Statistics
Matches: 333, Mismatches: 59, Indels: 16
0.82 0.14 0.04
Matches are distributed among these distances:
137 1 0.00
138 2 0.01
139 325 0.98
140 2 0.01
141 2 0.01
142 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (139 bp):
TTCCTACATAATGAGGACATCTAGCCATCTTTAGGGATAATTTGGAGACAACACGATTCCTACGT
GATGAGGAAGTCTGGTTATCTGAGGATGACGCTGCTCCTACGCGTTAAGGAGATCTAGTCAGTGG
ACGACATTA
Found at i:3043882 original size:51 final size:51
Alignment explanation
Indices: 3043803--3043904 Score: 177
Period size: 51 Copynumber: 2.0 Consensus size: 51
3043793 CGAAACTTTG
* *
3043803 TTTCGAGAGAAACGATCTCAAAGATTTATGTTTCAAGAGAAATTGTCTCAA
1 TTTCGAGAGAAACAATCTCAAAGATTTATGTTTCAAGAGAAACTGTCTCAA
*
3043854 TTTCGAGAGAAACAATCTCAAAGTTTTATGTTTCAAGAGAAACTGTCTCAA
1 TTTCGAGAGAAACAATCTCAAAGATTTATGTTTCAAGAGAAACTGTCTCAA
3043905 GCGAGACAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (51 bp):
TTTCGAGAGAAACAATCTCAAAGATTTATGTTTCAAGAGAAACTGTCTCAA
Found at i:3043932 original size:67 final size:67
Alignment explanation
Indices: 3043858--3044056 Score: 294
Period size: 67 Copynumber: 3.0 Consensus size: 67
3043848 TCTCAATTTC
*
3043858 GAGAGAAACAATCTCAAAGTTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTT
1 GAGAGAAACAATCTCAAAGATTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTT
3043923 TA
66 TA
* *
3043925 GAGAGAAACAATCTCAAAGATTTATGTTTCAAGTGAAACTGTCTCAAGCGAGACAAAACTTTTTT
1 GAGAGAAACAATCTCAAAGATTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTT
*
3043990 TC
66 TA
* * * * *
3043992 GAGAAAAACAATCTCAAAGGTTTATGTTT-ATAGAGAAAATGTCTTAAGCGAGATAAAA-TTTGT
1 GAGAGAAACAATCTCAAAGATTTATGTTTCA-AGAGAAACTGTCTCAAGCGAGACAAAACTTTGT
3044055 TT
65 TT
3044057 TTAGGGAAAA
Statistics
Matches: 120, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
66 7 0.06
67 113 0.94
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (67 bp):
GAGAGAAACAATCTCAAAGATTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTT
TA
Found at i:3044066 original size:36 final size:36
Alignment explanation
Indices: 3044016--3044092 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
3044006 CAAAGGTTTA
*
3044016 TGTTTATAGAGAAAATGTCTTAAGCGAGATAAAATT
1 TGTTTATAGAGAAAATGTATTAAGCGAGATAAAATT
* * * * * *
3044052 TGTTTTTAGGGAAAATTTATTAAGTGAGATCAATTT
1 TGTTTATAGAGAAAATGTATTAAGCGAGATAAAATT
3044088 TGTTT
1 TGTTT
3044093 CGAGTGAAAC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.35, C:0.04, G:0.19, T:0.42
Consensus pattern (36 bp):
TGTTTATAGAGAAAATGTATTAAGCGAGATAAAATT
Found at i:3044284 original size:99 final size:99
Alignment explanation
Indices: 3044120--3044408 Score: 337
Period size: 99 Copynumber: 2.9 Consensus size: 99
3044110 AAATTTGTGG
* * * * * *
3044120 AAAA-TGTCTCAGGCGAGACAAAATTTGTTTTGAGGAAAACAATCTCAATTAAGATAAAATTTGT
1 AAAACTGTCTCAAGTGAGACGAAATTTATTTTGA-G--AACAATCTCAAGTAAGATAAATTTTGT
* *
3044184 TTCAAGTGAAACAATTTTAGAATTTGTGTTTCAAAGA
63 TTCAAGTGAAACAATTTCAAAATTTGTGTTTCAAAGA
* * *
3044221 AAAACTGTCTCAAGTGAGATGAAATTTATTTTGAGAACAATCCCAAGTGAGATAAATTTTGTTTC
1 AAAACTGTCTCAAGTGAGACGAAATTTATTTTGAGAACAATCTCAAGTAAGATAAATTTTGTTTC
* *** *
3044286 AAGTGAAATAATTTCAAAATTTGTGTTTCTTGGG
66 AAGTGAAACAATTTCAAAATTTGTGTTTCAAAGA
* * * * * *
3044320 GAAACTGTCTCAAGTTAGACGAAATTTGTTTTGAGAACAATCTTAAGTTAGATAAATTTTGTTTT
1 AAAACTGTCTCAAGTGAGACGAAATTTATTTTGAGAACAATCTCAAGTAAGATAAATTTTGTTTC
*
3044385 GAGTGAAACAATTTCAAAATTTGT
66 AAGTGAAACAATTTCAAAATTTGT
3044409 ATTATAGGGG
Statistics
Matches: 161, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
99 132 0.82
101 5 0.03
102 24 0.15
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (99 bp):
AAAACTGTCTCAAGTGAGACGAAATTTATTTTGAGAACAATCTCAAGTAAGATAAATTTTGTTTC
AAGTGAAACAATTTCAAAATTTGTGTTTCAAAGA
Found at i:3056695 original size:11 final size:11
Alignment explanation
Indices: 3056679--3056739 Score: 63
Period size: 11 Copynumber: 5.7 Consensus size: 11
3056669 CGTTGATCGG
3056679 CGTTGACTGGC
1 CGTTGACTGGC
*
3056690 CGTTGACCGG-
1 CGTTGACTGGC
3056700 CGTTGACTGGC
1 CGTTGACTGGC
**
3056711 CGTTGACCAG-
1 CGTTGACTGGC
*
3056721 CATTGACTGGC
1 CGTTGACTGGC
*
3056732 CATTGACT
1 CGTTGACT
3056740 TTTTTTGGGT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
10 16 0.39
11 25 0.61
ACGTcount: A:0.15, C:0.28, G:0.31, T:0.26
Consensus pattern (11 bp):
CGTTGACTGGC
Found at i:3056695 original size:21 final size:21
Alignment explanation
Indices: 3056659--3056738 Score: 106
Period size: 21 Copynumber: 3.8 Consensus size: 21
3056649 TTAACCACTA
* *
3056659 TTGACTGGATCGTTGATCGGCG
1 TTGACTGG-CCGTTGACCGGCG
3056681 TTGACTGGCCGTTGACCGGCG
1 TTGACTGGCCGTTGACCGGCG
* *
3056702 TTGACTGGCCGTTGACCAGCA
1 TTGACTGGCCGTTGACCGGCG
*
3056723 TTGACTGGCCATTGAC
1 TTGACTGGCCGTTGAC
3056739 TTTTTTTGGG
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
21 45 0.85
22 8 0.15
ACGTcount: A:0.15, C:0.25, G:0.33, T:0.28
Consensus pattern (21 bp):
TTGACTGGCCGTTGACCGGCG
Found at i:3058648 original size:24 final size:24
Alignment explanation
Indices: 3058621--3058670 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
3058611 AAACAGTTAG
3058621 TACATGTAAGATAATCAATAGAAT
1 TACATGTAAGATAATCAATAGAAT
3058645 TACATGTAAGATAATCAATAGAAT
1 TACATGTAAGATAATCAATAGAAT
3058669 TA
1 TA
3058671 AAAGATGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.30
Consensus pattern (24 bp):
TACATGTAAGATAATCAATAGAAT
Found at i:3060434 original size:20 final size:19
Alignment explanation
Indices: 3060397--3060447 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
3060387 CAAACATGGA
* *
3060397 TAATAATATTTATTTAATG
1 TAATAATATATATATAATG
3060416 TAATACATATATATATAATATG
1 TAATA-ATATATATAT-A-ATG
3060438 TAA-AATATAT
1 TAATAATATAT
3060448 TCATACATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 5 0.19
20 14 0.52
21 2 0.07
22 6 0.22
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (19 bp):
TAATAATATATATATAATG
Found at i:3073741 original size:22 final size:21
Alignment explanation
Indices: 3073712--3073756 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
3073702 GGCCTACAAA
*
3073712 AACATAAA-ATATATTAATAAT
1 AACATAAATA-ATAATAATAAT
3073733 AACAGTAAATAATAATAATAAT
1 AACA-TAAATAATAATAATAAT
3073755 AA
1 AA
3073757 TTTAAAACCC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.19
22 16 0.76
23 1 0.05
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.29
Consensus pattern (21 bp):
AACATAAATAATAATAATAAT
Found at i:3076764 original size:20 final size:20
Alignment explanation
Indices: 3076721--3076771 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
3076711 AAACTTAGTC
* * * *
3076721 AACCCAAACCATCCTGCGTC
1 AACCCGAACCATCATGCCTA
3076741 AACCCGAACCATCATGCCTA
1 AACCCGAACCATCATGCCTA
3076761 AACCCGAACCA
1 AACCCGAACCA
3076772 GTATGACCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.43, G:0.10, T:0.12
Consensus pattern (20 bp):
AACCCGAACCATCATGCCTA
Found at i:3076821 original size:19 final size:18
Alignment explanation
Indices: 3076779--3076828 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
3076769 CCAGTATGAC
*
3076779 CCGTTGACTTTGACCTGG
1 CCGTTGACTTTGACCTGA
* *
3076797 CCGTTGACTTTGTCTTTGA
1 CCGTTGACTTTGAC-CTGA
*
3076816 CCGTTGAATTTGA
1 CCGTTGACTTTGA
3076829 ACAAAAAGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 13 0.50
19 13 0.50
ACGTcount: A:0.14, C:0.22, G:0.24, T:0.40
Consensus pattern (18 bp):
CCGTTGACTTTGACCTGA
Found at i:3081302 original size:12 final size:13
Alignment explanation
Indices: 3081285--3081319 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
3081275 TACATATGTA
3081285 ATTTAAGT-ATTT
1 ATTTAAGTGATTT
3081297 ATTTAAGTGATTT
1 ATTTAAGTGATTT
*
3081310 AATTAAGTGA
1 ATTTAAGTGA
3081320 ATCTCTTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 8 0.38
13 13 0.62
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (13 bp):
ATTTAAGTGATTT
Found at i:3085070 original size:26 final size:28
Alignment explanation
Indices: 3085041--3085094 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
3085031 TAATTATTCC
3085041 ATTTGTAA-T-ATTTTA-TGCTAAAATGA
1 ATTTGTAATTCATTTTATTGC-AAAATGA
*
3085067 ATTTTTAATTCATTTTATTGCAAAATGA
1 ATTTGTAATTCATTTTATTGCAAAATGA
3085095 CTTTTTGCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 7 0.29
27 1 0.04
28 13 0.54
29 3 0.12
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.48
Consensus pattern (28 bp):
ATTTGTAATTCATTTTATTGCAAAATGA
Found at i:3086475 original size:20 final size:18
Alignment explanation
Indices: 3086432--3086480 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
3086422 AATTGGATTC
3086432 TTGTTTTATAAATTGTAA
1 TTGTTTTATAAATTGTAA
* *
3086450 TAGTTTTATAATTTGAGTAA
1 TTGTTTTATAAATT--GTAA
3086470 TTGTTTT-TAAA
1 TTGTTTTATAAA
3086481 GTGATAATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 12 0.48
19 3 0.12
20 10 0.40
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (18 bp):
TTGTTTTATAAATTGTAA
Found at i:3087574 original size:62 final size:62
Alignment explanation
Indices: 3087489--3087679 Score: 217
Period size: 62 Copynumber: 3.1 Consensus size: 62
3087479 ATCATTTGAT
* * *
3087489 GAAAGGGATCGATCTTTTTTCAAATGATTTGACCGTTTCAATAAAGATACTGATCCTTTAGG
1 GAAAGCGATCGATCTTTTTTCAAATAATTTGACCGTTTCAATAAAGATATTGATCCTTTAGG
* * **
3087551 GAAAGTGATCAATCTTTTTTCAAATAATTTGA-TATTTGCAATAAAGAGT-TTGATCCTTTAGG
1 GAAAGCGATCGATCTTTTTTCAAATAATTTGACCGTTT-CAATAAAGA-TATTGATCCTTTAGG
* * * * * *
3087613 GAAAGCAATCGATCCTTTCTCAAATAATTTAACCGTTGC-ATGAAAGAGATTGATCCTTTAGG
1 GAAAGCGATCGATCTTTTTTCAAATAATTTGACCGTTTCAAT-AAAGATATTGATCCTTTAGG
3087675 GAAAG
1 GAAAG
3087680 GGGTTAGTCA
Statistics
Matches: 108, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
61 5 0.05
62 100 0.93
63 3 0.03
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.35
Consensus pattern (62 bp):
GAAAGCGATCGATCTTTTTTCAAATAATTTGACCGTTTCAATAAAGATATTGATCCTTTAGG
Found at i:3092299 original size:17 final size:17
Alignment explanation
Indices: 3092277--3092315 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
3092267 TCCCTTTAGG
3092277 TATCCATAAATATATGA
1 TATCCATAAATATATGA
3092294 TATCCATAAATATATGA
1 TATCCATAAATATATGA
3092311 TATCC
1 TATCC
3092316 TTATTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (17 bp):
TATCCATAAATATATGA
Found at i:3092592 original size:20 final size:20
Alignment explanation
Indices: 3092567--3092614 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
3092557 TTCTAGATTC
*
3092567 TTTTTCTTA-AAATTATTTAA
1 TTTTTCTTACAAATCA-TTAA
3092587 TTTTTCTTACAAATCATTAA
1 TTTTTCTTACAAATCATTAA
*
3092607 TCTTTCTT
1 TTTTTCTT
3092615 TCAAGTTCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTTCTTACAAATCATTAA
Found at i:3094420 original size:34 final size:32
Alignment explanation
Indices: 3094367--3094436 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
3094357 CATTACAAAC
*
3094367 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
3094399 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
3094433 TCCC
1 TCCC
3094437 CTTTATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:3094843 original size:41 final size:40
Alignment explanation
Indices: 3094786--3094886 Score: 175
Period size: 41 Copynumber: 2.5 Consensus size: 40
3094776 CGTTAGACAA
3094786 GGGGAATCGGTACCCCCTGGGGGGGAATCTGTACCCCTGGG
1 GGGGAATCGGTACCCCCTGGGGGGGAATCTGTACCCCT-GG
3094827 GGGGAATCGGTACCCCCTGGGGGGGAATCTGTACCCCTGG
1 GGGGAATCGGTACCCCCTGGGGGGGAATCTGTACCCCTGG
* *
3094867 GGGGAAACTGTACCCCCTGG
1 GGGGAATCGGTACCCCCTGG
3094887 ACAATCTGAT
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
40 20 0.34
41 38 0.66
ACGTcount: A:0.16, C:0.28, G:0.40, T:0.17
Consensus pattern (40 bp):
GGGGAATCGGTACCCCCTGGGGGGGAATCTGTACCCCTGG
Found at i:3094883 original size:20 final size:21
Alignment explanation
Indices: 3094786--3094886 Score: 154
Period size: 21 Copynumber: 5.0 Consensus size: 21
3094776 CGTTAGACAA
*
3094786 GGGGAATCGGTACCCCCTGGG
1 GGGGAATCTGTACCCCCTGGG
3094807 GGGGAATCTGTA-CCCCTGGG
1 GGGGAATCTGTACCCCCTGGG
*
3094827 GGGGAATCGGTACCCCCTGGG
1 GGGGAATCTGTACCCCCTGGG
3094848 GGGGAATCTGTA-CCCCT-GG
1 GGGGAATCTGTACCCCCTGGG
*
3094867 GGGGAAACTGTACCCCCTGG
1 GGGGAATCTGTACCCCCTGG
3094887 ACAATCTGAT
Statistics
Matches: 73, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
19 13 0.18
20 29 0.40
21 31 0.42
ACGTcount: A:0.16, C:0.28, G:0.40, T:0.17
Consensus pattern (21 bp):
GGGGAATCTGTACCCCCTGGG
Found at i:3096339 original size:19 final size:20
Alignment explanation
Indices: 3096298--3096345 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
3096288 TCTAAATCCT
*
3096298 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
*
3096318 TTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
3096337 TTTTCAAAA
1 TTTTCAAAA
3096346 GGAAAATTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.29, C:0.10, G:0.06, T:0.54
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:3099142 original size:42 final size:44
Alignment explanation
Indices: 3099095--3099177 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 44
3099085 TCTTTTGTGG
*
3099095 CGTTTG-T-AAAAAAACGTCGGTAAATGTTC-TGACATATAGTGT
1 CGTTTGTTCAAAAAAACGTCGGTAAAAG-TCATGACATATAGTGT
**
3099137 CGTTTGTTCCCAAAAACGTCGGTAAAAGTCATGACATATAG
1 CGTTTGTTCAAAAAAACGTCGGTAAAAGTCATGACATATAG
3099178 CAACATTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 6 0.17
43 3 0.09
44 26 0.74
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (44 bp):
CGTTTGTTCAAAAAAACGTCGGTAAAAGTCATGACATATAGTGT
Found at i:3099187 original size:44 final size:44
Alignment explanation
Indices: 3099104--3099187 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
3099094 GCGTTTGTAA
* *** *
3099104 AAAAACGTCGGTAAATGTTCTGACATATAGTGTCGTTTGTTCCC
1 AAAAACGTCGGTAAAAGTTCTGACATATAGCAACATTTGTTCCC
3099148 AAAAACGTCGGTAAAAG-TCATGACATATAGCAACATTTGT
1 AAAAACGTCGGTAAAAGTTC-TGACATATAGCAACATTTGT
3099188 AAATTTAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 2 0.06
44 32 0.94
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.30
Consensus pattern (44 bp):
AAAAACGTCGGTAAAAGTTCTGACATATAGCAACATTTGTTCCC
Found at i:3101005 original size:31 final size:30
Alignment explanation
Indices: 3100968--3101025 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
3100958 CTATATAAGA
*
3100968 AATAATTAAATGTAAGTTTTCAAA-ATTAACC
1 AATAATTAAA-GAAAG-TTTCAAACATTAACC
3100999 AATAATTAAAGAAAGTTTCAAACATTA
1 AATAATTAAAGAAAGTTTCAAACATTA
3101026 CCTTCAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 7 0.28
30 8 0.32
31 10 0.40
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.33
Consensus pattern (30 bp):
AATAATTAAAGAAAGTTTCAAACATTAACC
Found at i:3103144 original size:26 final size:26
Alignment explanation
Indices: 3103108--3103161 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
3103098 CGTCGCTTAC
3103108 CCTTGACAAATCCATCCAACTGTTAT
1 CCTTGACAAATCCATCCAACTGTTAT
3103134 CCTTGACAAATCCATCCAACTGTTAT
1 CCTTGACAAATCCATCCAACTGTTAT
3103160 CC
1 CC
3103162 ATTTCGTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.30, C:0.33, G:0.07, T:0.30
Consensus pattern (26 bp):
CCTTGACAAATCCATCCAACTGTTAT
Found at i:3103980 original size:29 final size:25
Alignment explanation
Indices: 3103909--3103960 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
3103899 GTCATAAGCC
3103909 TAGAATGTACATTTCATTGATTTTT
1 TAGAATGTACATTTCATTGATTTTT
3103934 TAGAATGTACATTTCATTGATTTTT
1 TAGAATGTACATTTCATTGATTTTT
3103959 TA
1 TA
3103961 TGATCATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.29, C:0.08, G:0.12, T:0.52
Consensus pattern (25 bp):
TAGAATGTACATTTCATTGATTTTT
Found at i:3104627 original size:15 final size:14
Alignment explanation
Indices: 3104607--3104640 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 14
3104597 ATACATACTG
3104607 ATACACATATGCACT
1 ATACACATATGCA-T
3104622 ATACACATATGCAT
1 ATACACATATGCAT
3104636 ATACA
1 ATACA
3104641 TTTGAAAGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.44, C:0.24, G:0.06, T:0.26
Consensus pattern (14 bp):
ATACACATATGCAT
Found at i:3106224 original size:43 final size:42
Alignment explanation
Indices: 3106169--3106252 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 42
3106159 GTCACAAAGG
* * * *
3106169 TACATGACTATTGTGGCGTTTATTACAAAAAACGCTACTAAAT
1 TACATGACTATTGCGACGTTTACTAC-AAAAACGCCACTAAAT
* *
3106212 TACATGATTATTGCGATGTTTACTACAAAAACGCCACTAAA
1 TACATGACTATTGCGACGTTTACTACAAAAACGCCACTAAA
3106253 GTAGAAGTCT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
42 14 0.40
43 21 0.60
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (42 bp):
TACATGACTATTGCGACGTTTACTACAAAAACGCCACTAAAT
Found at i:3106287 original size:41 final size:40
Alignment explanation
Indices: 3106238--3106361 Score: 135
Period size: 41 Copynumber: 3.0 Consensus size: 40
3106228 TGTTTACTAC
*
3106238 AAAAACGCCACTAAAGTA-GAAGTCTATAGCGGTGATTGTA
1 AAAAACGCCACTAAAGTATG-AGTCTATAGCGGCGATTGTA
*
3106278 TAAAAACGCCACTAAAGTATGAGTCTATAGCGGCGTTTGTA
1 -AAAAACGCCACTAAAGTATGAGTCTATAGCGGCGATTGTA
* * * * *
3106319 AACAAACGCCACGAAACTCTAAGTCTTTAGCGGC-ATTTGTA
1 AA-AAACGCCACTAAAGTATGAGTCTATAGCGGCGA-TTGTA
3106360 AA
1 AA
3106362 CGCCACTAAT
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
40 2 0.03
41 69 0.96
42 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (40 bp):
AAAAACGCCACTAAAGTATGAGTCTATAGCGGCGATTGTA
Found at i:3106640 original size:83 final size:83
Alignment explanation
Indices: 3106501--3106777 Score: 281
Period size: 82 Copynumber: 3.3 Consensus size: 83
3106491 TGCTCATTCT
* * * * *
3106501 GGCGTTTGTATAAAAACGCCGCTAAATTACTACTCTATTGCGGCGTTTGTTCAAAAAATACCACT
1 GGCGTTTGTATAAAAACGCCGCTAAAGTACTACTCTGTTGCAGCGTTTGTTGAAAAAATGCCACT
3106566 ATATAAGTACCCTATTGC
66 ATATAAGTACCCTATTGC
* * * *
3106584 GGCGTTTGTATAAAAACGCCGCTAAAGTACTACTCTGGTGCAGCGGTTGTTG-AAAAATGTCATT
1 GGCGTTTGTATAAAAACGCCGCTAAAGTACTACTCTGTTGCAGCGTTTGTTGAAAAAATGCCACT
* * *
3106648 ATATATGAACCCTATTAC
66 ATATAAGTACCCTATTGC
* * * ** * * *
3106666 GGCATTTGTATAACAACACTACTAACA-TACTACTCTGTTGTAGCATTTTGTTGAAAAAACGCCA
1 GGCGTTTGTATAAAAACGCCGCTAA-AGTACTACTCTGTTGCAGC-GTTTGTTGAAAAAATGCCA
* * * * *
3106730 CTATA-GATTAATCATATTGT
64 CTATATAAGT-ACCCTATTGC
3106750 GGCGTTTGTATAAAAACGCCGCTAAAGT
1 GGCGTTTGTATAAAAACGCCGCTAAAGT
3106778 TACCATTTTG
Statistics
Matches: 152, Mismatches: 37, Indels: 9
0.77 0.19 0.05
Matches are distributed among these distances:
82 59 0.39
83 54 0.36
84 39 0.26
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Consensus pattern (83 bp):
GGCGTTTGTATAAAAACGCCGCTAAAGTACTACTCTGTTGCAGCGTTTGTTGAAAAAATGCCACT
ATATAAGTACCCTATTGC
Found at i:3107315 original size:14 final size:14
Alignment explanation
Indices: 3107298--3107336 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
3107288 ATAATATGAA
3107298 AATAAAAATATTTT
1 AATAAAAATATTTT
*
3107312 AATAATTAATATTTT
1 AATAA-AAATATTTT
*
3107327 ATTAAAAATA
1 AATAAAAATA
3107337 ATACTAGACT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATAAAAATATTTT
Found at i:3107391 original size:10 final size:9
Alignment explanation
Indices: 3107373--3107407 Score: 54
Period size: 10 Copynumber: 3.9 Consensus size: 9
3107363 ATGTATAAAG
3107373 TAATATTAA
1 TAATATTAA
3107382 TAATTATTAA
1 TAA-TATTAA
3107392 TAAT-TTAA
1 TAATATTAA
3107400 TAATATTA
1 TAATATTA
3107408 TTTTTATGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 8 0.33
9 7 0.29
10 9 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
TAATATTAA
Found at i:3108595 original size:16 final size:16
Alignment explanation
Indices: 3108576--3108630 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
3108566 ACCTGAACCG
3108576 AAAGCAACTCGAATCA
1 AAAGCAACTCGAATCA
* *
3108592 AAAGTAACTTGAAT-A
1 AAAGCAACTCGAATCA
**
3108607 AAAAAAACTCGAATTC-
1 AAAGCAACTCGAA-TCA
3108623 AAAGCAAC
1 AAAGCAAC
3108631 CCAAATTTAG
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
15 11 0.37
16 19 0.63
ACGTcount: A:0.55, C:0.18, G:0.11, T:0.16
Consensus pattern (16 bp):
AAAGCAACTCGAATCA
Found at i:3110123 original size:22 final size:23
Alignment explanation
Indices: 3110098--3110159 Score: 63
Period size: 27 Copynumber: 2.5 Consensus size: 23
3110088 CTTAATTTAG
3110098 AAATATTTTAATT-TTAAAAATA
1 AAATATTTTAATTATTAAAAATA
*
3110120 AAATATTTCTAAATTAAGTTAATAATA
1 AAATATTT-T-AATT-A-TTAAAAATA
3110147 AAATATATTTAAT
1 AAATAT-TTTAAT
3110160 AAGTTAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 8 0.24
23 1 0.03
24 4 0.12
26 3 0.09
27 15 0.45
28 2 0.06
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
AAATATTTTAATTATTAAAAATA
Found at i:3110147 original size:27 final size:25
Alignment explanation
Indices: 3110111--3110168 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 25
3110101 TATTTTAATT
*
3110111 TTAAAAATAAAATAT-TTCTAAATTAAG
1 TTAATAATAAAATATATT-T-AA-TAAG
3110138 TTAATAATAAAATATATTTAATAAG
1 TTAATAATAAAATATATTTAATAAG
3110163 TTAATA
1 TTAATA
3110169 TAGAAAAACG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 10 0.34
26 2 0.07
27 15 0.52
28 2 0.07
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (25 bp):
TTAATAATAAAATATATTTAATAAG
Found at i:3111437 original size:20 final size:21
Alignment explanation
Indices: 3111412--3111450 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3111402 GATAATTTTA
*
3111412 AAAATTTTA-ATTAAAAAAAT
1 AAAATTATATATTAAAAAAAT
3111432 AAAATTATATATTAAAAAA
1 AAAATTATATATTAAAAAA
3111451 CTCAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAATTATATATTAAAAAAAT
Found at i:3115164 original size:17 final size:17
Alignment explanation
Indices: 3115123--3115189 Score: 73
Period size: 17 Copynumber: 3.9 Consensus size: 17
3115113 ATTCATGCAT
3115123 CTAGTTCATTGAA-TAAA
1 CTAGTTCATT-AATTAAA
*
3115140 GTTAGTTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
* *
3115158 CTAGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
*
3115175 CTAGTTCATTTATTA
1 CTAGTTCATTAATTA
3115190 GATAACTCTT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
17 29 0.69
18 13 0.31
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:3116510 original size:13 final size:13
Alignment explanation
Indices: 3116492--3116542 Score: 75
Period size: 13 Copynumber: 3.8 Consensus size: 13
3116482 CAAAGTCAAC
3116492 GAGTTGACTCAGT
1 GAGTTGACTCAGT
3116505 GAGTTGACTCAGT
1 GAGTTGACTCAGT
*
3116518 GAGTTGACTCAAT
1 GAGTTGACTCAGT
*
3116531 CAAGTTGACTCA
1 -GAGTTGACTCA
3116543 ATGGCTGATT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
13 25 0.71
14 10 0.29
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (13 bp):
GAGTTGACTCAGT
Found at i:3116538 original size:14 final size:13
Alignment explanation
Indices: 3116487--3116545 Score: 73
Period size: 13 Copynumber: 4.5 Consensus size: 13
3116477 TCAAACAAAG
*
3116487 TCAACGAGTTGAC
1 TCAATGAGTTGAC
*
3116500 TCAGTGAGTTGAC
1 TCAATGAGTTGAC
*
3116513 TCAGTGAGTTGAC
1 TCAATGAGTTGAC
*
3116526 TCAATCAAGTTGAC
1 TCAAT-GAGTTGAC
3116540 TCAATG
1 TCAATG
3116546 GCTGATTCGG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
13 28 0.70
14 12 0.30
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (13 bp):
TCAATGAGTTGAC
Found at i:3119717 original size:218 final size:219
Alignment explanation
Indices: 3119332--3119758 Score: 847
Period size: 218 Copynumber: 2.0 Consensus size: 219
3119322 AATTGATACC
3119332 TTAGGACCCCTTTTTATTCAAGTGCATTAGGAAGGTTTTCATGAACCTTAAATCAGAATAATTCT
1 TTAGGACCCCTTTTTATTCAAGTGCATTAGGAAGGTTTTCATGAACCTTAAATCAGAATAATTCT
3119397 AGACTCAGATTTACAGAGAGTGATTCCATTACTTTAACGATCAGGGTATTCAGGATTATTTATTG
66 AGACTCAGATTTACAGAGAGTGATTCCATTACTTTAACGATCAGGGTATTCAGGATTATTTATTG
3119462 AATTATCAGGATTTTGAGTCCAGCTGAACCAATGATCTCAACACTGCAATACTTTTCAATCATTC
131 AATTATCAGGATTTTGAGTCCAGCTGAACCAATGATCTCAACACTGCAATACTTTTCAATCATTC
3119527 AGGTTGTGATACTTTATATTCACT
196 AGGTTGTGATACTTTATATTCACT
3119551 TTAGGA-CCCTTTTTATTCAAGTGCATTAGGAAGGTTTTCATGAACCTTAAATCAGAATAATTCT
1 TTAGGACCCCTTTTTATTCAAGTGCATTAGGAAGGTTTTCATGAACCTTAAATCAGAATAATTCT
3119615 AGACTCAGATTTACAGAGAGTGATTCCATTACTTTAACGATCAGGGTATTCAGGATTATTTATTG
66 AGACTCAGATTTACAGAGAGTGATTCCATTACTTTAACGATCAGGGTATTCAGGATTATTTATTG
3119680 AATTATCAGGATTTTGAGTCCAGCTGAACCAATGATCTCAACACTGCAATACTTTTCAATCATTC
131 AATTATCAGGATTTTGAGTCCAGCTGAACCAATGATCTCAACACTGCAATACTTTTCAATCATTC
3119745 AGGTTGTGATACTT
196 AGGTTGTGATACTT
3119759 CATTATTATT
Statistics
Matches: 208, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
218 202 0.97
219 6 0.03
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (219 bp):
TTAGGACCCCTTTTTATTCAAGTGCATTAGGAAGGTTTTCATGAACCTTAAATCAGAATAATTCT
AGACTCAGATTTACAGAGAGTGATTCCATTACTTTAACGATCAGGGTATTCAGGATTATTTATTG
AATTATCAGGATTTTGAGTCCAGCTGAACCAATGATCTCAACACTGCAATACTTTTCAATCATTC
AGGTTGTGATACTTTATATTCACT
Found at i:3122477 original size:2 final size:2
Alignment explanation
Indices: 3122470--3122518 Score: 66
Period size: 2 Copynumber: 25.0 Consensus size: 2
3122460 AAGCTTTTAT
*
3122470 TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TGA TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
3122512 TA -A TA TA
1 TA TA TA TA
3122519 AAGTTAAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
1 2 0.05
2 38 0.90
3 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:3122493 original size:13 final size:13
Alignment explanation
Indices: 3122470--3122518 Score: 73
Period size: 13 Copynumber: 3.8 Consensus size: 13
3122460 AAGCTTTTAT
3122470 TATAT-ATATATA
1 TATATAATATATA
3122482 TATATAATATATA
1 TATATAATATATA
* *
3122495 TATATGATATAGA
1 TATATAATATATA
3122508 TATATAATATA
1 TATATAATATA
3122519 AAGTTAAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
12 5 0.15
13 28 0.85
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (13 bp):
TATATAATATATA
Found at i:3122493 original size:15 final size:15
Alignment explanation
Indices: 3122473--3122519 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
3122463 CTTTTATTAT
3122473 ATATATATATATATA
1 ATATATATATATATA
3122488 ATATATATATATGAT-
1 ATATATATATAT-ATA
*
3122503 ATAGATATATAATATA
1 ATATATATAT-ATATA
3122519 A
1 A
3122520 AGTTAAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 23 0.82
16 5 0.18
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:3129397 original size:6 final size:7
Alignment explanation
Indices: 3129387--3129431 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
3129377 ACGGTCAAAG
3129387 TCAACGA
1 TCAACGA
3129394 -CAACGA
1 TCAACGA
*
3129400 TCAACGG
1 TCAACGA
*
3129407 TCAATG-
1 TCAACGA
3129413 TCAACGA
1 TCAACGA
3129420 TCAACGA
1 TCAACGA
3129427 TCAAC
1 TCAAC
3129432 AATTATGTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
6 11 0.33
7 22 0.67
ACGTcount: A:0.40, C:0.29, G:0.16, T:0.16
Consensus pattern (7 bp):
TCAACGA
Found at i:3129405 original size:26 final size:27
Alignment explanation
Indices: 3129376--3129431 Score: 96
Period size: 26 Copynumber: 2.1 Consensus size: 27
3129366 AACGTCGGTT
3129376 AACGGTCAAAGTCAACGA-CAACGATC
1 AACGGTCAAAGTCAACGATCAACGATC
*
3129402 AACGGTCAATGTCAACGATCAACGATC
1 AACGGTCAAAGTCAACGATCAACGATC
3129429 AAC
1 AAC
3129432 AATTATGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 17 0.61
27 11 0.39
ACGTcount: A:0.41, C:0.27, G:0.18, T:0.14
Consensus pattern (27 bp):
AACGGTCAAAGTCAACGATCAACGATC
Found at i:3132630 original size:96 final size:96
Alignment explanation
Indices: 3132466--3132657 Score: 366
Period size: 96 Copynumber: 2.0 Consensus size: 96
3132456 GAATAAAAAA
*
3132466 ATGCATTAGTAATAATAAATTTTTTGTTATAAAAATTTGTGAAAATGCTATTCACAAGATTTTAC
1 ATGCATTAGTAATAATAAATTTTTGGTTATAAAAATTTGTGAAAATGCTATTCACAAGATTTTAC
*
3132531 ATTTTAATTGGTCGCAAGATTCTAAATCATT
66 ATTTTAATTGGTAGCAAGATTCTAAATCATT
3132562 ATGCATTAGTAATAATAAATTTTTGGTTATAAAAATTTGTGAAAATGCTATTCACAAGATTTTAC
1 ATGCATTAGTAATAATAAATTTTTGGTTATAAAAATTTGTGAAAATGCTATTCACAAGATTTTAC
3132627 ATTTTAATTGGTAGCAAGATTCTAAATCATT
66 ATTTTAATTGGTAGCAAGATTCTAAATCATT
3132658 TTGACAATAA
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 94 1.00
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (96 bp):
ATGCATTAGTAATAATAAATTTTTGGTTATAAAAATTTGTGAAAATGCTATTCACAAGATTTTAC
ATTTTAATTGGTAGCAAGATTCTAAATCATT
Found at i:3137134 original size:17 final size:17
Alignment explanation
Indices: 3137112--3137195 Score: 96
Period size: 17 Copynumber: 4.9 Consensus size: 17
3137102 AATTAAGAGT
3137112 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* * *
3137129 TAGTTTGATGAATGAAA
1 TAGTTTAATAAATGAAC
*
3137146 TAGTTTAATGAATGAAC
1 TAGTTTAATAAATGAAC
*
3137163 TAGTTTAATCAATGAAC
1 TAGTTTAATAAATGAAC
* **
3137180 TACTTTGTTAAATGAA
1 TAGTTTAATAAATGAA
3137196 GTGCATAGCT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 57 1.00
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.37
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:3137151 original size:34 final size:34
Alignment explanation
Indices: 3137112--3137178 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
3137102 AATTAAGAGT
* *
3137112 TAGTTTAATAAATGAACTAGTTTGATGAATGAAA
1 TAGTTTAATAAATGAACTAGTTTAATCAATGAAA
*
3137146 TAGTTTAATGAATGAACTAGTTTAATCAATGAA
1 TAGTTTAATAAATGAACTAGTTTAATCAATGAA
3137179 CTACTTTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.36
Consensus pattern (34 bp):
TAGTTTAATAAATGAACTAGTTTAATCAATGAAA
Found at i:3137821 original size:23 final size:23
Alignment explanation
Indices: 3137788--3137831 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
3137778 AATAATTCTA
3137788 CTTTTATGACACATTTTTATTTGT
1 CTTTTATGACACA-TTTTATTTGT
*
3137812 CTTTT-TGACATATTTTATTT
1 CTTTTATGACACATTTTATTT
3137832 TACCTTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 6 0.32
24 5 0.26
ACGTcount: A:0.20, C:0.11, G:0.07, T:0.61
Consensus pattern (23 bp):
CTTTTATGACACATTTTATTTGT
Found at i:3137839 original size:22 final size:21
Alignment explanation
Indices: 3137798--3137843 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
3137788 CTTTTATGAC
*
3137798 ACATTTTTATTTGTCTTTTTG
1 ACATTTTTATTTGTCCTTTTG
3137819 ACATATTTTATTT-TACCTTTTG
1 ACAT-TTTTATTTGT-CCTTTTG
3137841 ACA
1 ACA
3137844 AGTTTTTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.22, C:0.13, G:0.07, T:0.59
Consensus pattern (21 bp):
ACATTTTTATTTGTCCTTTTG
Found at i:3138053 original size:3 final size:3
Alignment explanation
Indices: 3138045--3138080 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3138035 CACTTGAATA
3138045 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3138081 ATTTATGCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3143114 original size:16 final size:16
Alignment explanation
Indices: 3143093--3143126 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3143083 TTGTTTTTTG
3143093 TTTTATTTAT-TCATTT
1 TTTTATTT-TCTCATTT
3143109 TTTTATTTTCTCATTT
1 TTTTATTTTCTCATTT
3143125 TT
1 TT
3143127 AAATTTCATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 16 0.94
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTATTTTCTCATTT
Found at i:3144068 original size:47 final size:47
Alignment explanation
Indices: 3144017--3144118 Score: 150
Period size: 47 Copynumber: 2.2 Consensus size: 47
3144007 CCCGAAATCA
** * *
3144017 GCTCTAGTTGTTATGCAATAAAGAATTGCTAGAGTTGCCCAAAACTG
1 GCTCTAGTTGTTACACAATAAAGAATTGCTAGAGGTACCCAAAACTG
* *
3144064 GCTCTAGTTGTTACACATTCAAGAATTGCTAGAGGTACCCAAAACTG
1 GCTCTAGTTGTTACACAATAAAGAATTGCTAGAGGTACCCAAAACTG
3144111 GCTCTAGT
1 GCTCTAGT
3144119 CGACTAAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (47 bp):
GCTCTAGTTGTTACACAATAAAGAATTGCTAGAGGTACCCAAAACTG
Found at i:3153814 original size:20 final size:20
Alignment explanation
Indices: 3153789--3153826 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3153779 TCTAGGTTCA
*
3153789 AGTATCGATATTGGATGAAT
1 AGTATCGATATTAGATGAAT
3153809 AGTATCGATATTAGATGA
1 AGTATCGATATTAGATGA
3153827 TTTGGGATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (20 bp):
AGTATCGATATTAGATGAAT
Found at i:3156362 original size:2 final size:2
Alignment explanation
Indices: 3156353--3156391 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
3156343 TATATTTTCA
3156353 AT AT -T 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
3156392 TAATCTTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3164412 original size:3 final size:3
Alignment explanation
Indices: 3164397--3164440 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
3164387 CTAAATGTTT
* *
3164397 ATA ATA ATT ATA ATA ATA ATA ATA ATTA ATA ATA ATA GTA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA A
3164441 ATCAAAATGG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:3164969 original size:110 final size:112
Alignment explanation
Indices: 3164695--3165408 Score: 862
Period size: 110 Copynumber: 6.5 Consensus size: 112
3164685 GTTGGATGAG
* * *
3164695 TTCTTCTCATTATGAACTTCTTCATCCTTCTTTC-GATGAGTTCTTCTCTTTATGGAC-TTCTCT
1 TTCTTCTCATTATGAAC-TCTTCTTCCTTC-TTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
* ** * *
3164758 AGAAAATTTGATCCATCAAGTGATGGATTTGAGCAAAA--TCTGAACAAA
64 GGAAAAGCTAATCCATCAAGTGATGGATTTCAGCAAAAGGT-TGAACAAA
* * ****
3164806 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTT-TTCTTATTATGAACTCGAACTG
1 TTCTTCTCATTATGAAC-TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
** * *
3164870 GAAAAGCTAATTTATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
65 GAAAAGCTAATCCATCAAGTGATGGATTTCAGCAAAAGGTTGAACAAA
* *
3164918 TTCTTCTCATTATG-ACTCTTCTTCCTTCTTCAGATGAGTTCTTTTCA-TATGAACTTTTTCTGG
1 TTCTTCTCATTATGAACTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
* * * * *
3164981 AAAGGCTGATCCATCAATTGAT-GAATTCAGGTAAAAGGTTGAACAAA
66 AAAAGCTAATCCATCAAGTGATGGATTTCA-GCAAAAGGTTGAACAAA
*
3165028 TTCTTCTCA-T-TGAATTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
1 TTCTTCTCATTATGAACTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
* *
3165091 CAAAGCTAATCCATCAAGTGAT-GA-TTCAGCATAAGGTTGAACAAA
66 AAAAGCTAATCCATCAAGTGATGGATTTCAGCAAAAGGTTGAACAAA
3165136 TTCTTCT-A-TATGAA-T-TT-TT-CTTCTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTCTTCTTCCTTC-TTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
3165195 GCAAAGCTAATCCATCAAGTGATGGA-TTCAGGCAAAAGG-TGAACAAA
65 GAAAAGCTAATCCATCAAGTGATGGATTTCA-GCAAAAGGTTGAACAAA
*
3165242 TTCTTCTCATTATGAATTTCTT-TTCCTTCTTCAGATGAGTTCTTCT-ATTATGAAC-TTCTCTG
1 TTCTTCTCATTATGAA-CTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * *
3165304 GAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAG
65 GAAAAGCTAATCCATCAAGTGATGGATTTCAGCAAAAGGTTGAACAAA
* *
3165352 CTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC-TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
3165409 CTAACTGACA
Statistics
Matches: 533, Mismatches: 47, Indels: 45
0.85 0.08 0.07
Matches are distributed among these distances:
104 4 0.01
105 60 0.11
106 23 0.04
107 11 0.02
108 34 0.06
109 79 0.15
110 164 0.31
111 122 0.23
112 35 0.07
113 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.39
Consensus pattern (112 bp):
TTCTTCTCATTATGAACTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
AAAAGCTAATCCATCAAGTGATGGATTTCAGCAAAAGGTTGAACAAA
Found at i:3165349 original size:324 final size:332
Alignment explanation
Indices: 3164695--3165408 Score: 908
Period size: 324 Copynumber: 2.2 Consensus size: 332
3164685 GTTGGATGAG
* * *
3164695 TTCTTCTCATTATGAACTTCTTCATCCTTCTTTC-GATGAGTTCTTCTCTTTATGGACTTCTCTA
1 TTCTTCTCATTATGAACTTCTTCTTCCTTC-TTCAGATGAGTTCTTCTCATTATGAACTTCTCTA
** * *
3164759 GAAAATTTGATCCATCAAGTGATGGATTTGAGCAAAATCTGAACAAATTCTTCTCATTATGAACT
65 GAAAAGCTAATCCATCAAGTGATGGATTTCAGCAAAATCTGAACAAATTCTTCTCATTATGAACT
* **
3164824 TCTTCATCCTTCTTCAGATGAGTTTTCTTATTATGAACTCGAACTGGAAAAGCTAATTTATCAAG
130 TCTT-ATCCTTCTTCAGATGAGTTTTCTCATTATGAACTCGAACTGGAAAAGCTAATCCATCAAG
*
3164889 TGATAGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGACTCTTCTTCCTTCTTCAGATG
194 TGATAGATTAGAGCAAAAGGTTGAACAAATTCTTCTCATTATGACTCTTCTTCCTTCTTCAGATG
* * * * *
3164954 AGTTCTTTTCATATGAACTTTTTCTGGAAAGGCTGATCCATCAATTGATGAATTCAGGTAAAAGG
259 AGTTCTTCTCATATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAGGCAAAAGG
3165019 TTGAACAAA
324 TTGAACAAA
*
3165028 TTCTTCTCA-T-TGAA-TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTA
* *
3165090 GCAAAGCTAATCCATCAAGTGAT-GA-TTCAGCATAAGGT-TGAACAAATTCTTCT-A-TATGAA
65 GAAAAGCTAATCCATCAAGTGATGGATTTCAGCA-AA-ATCTGAACAAATTCTTCTCATTATGAA
**** *
3165150 -TT-TT-T-CTTCTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTAATCCATC
128 CTTCTTATCCTTC-TTCAGATGAGTT-TTCTCATTATGAACTCGAACTGGAAAAGCTAATCCATC
* *
3165211 AAGTGATGGATTCAG-GCAAAAGG-TGAACAAATTCTTCTCATTATGAAT-TTCTTTTCCTTCTT
191 AAGTGATAGATT-AGAGCAAAAGGTTGAACAAATTCTTCTCATTATGACTCTTC--TTCCTTCTT
* *
3165273 CAGATGAGTTCTTCT-ATTATGAAC-TTCTCTGGAAAAGCTGATCCATCAAATGATGGATT-TGA
253 CAGATGAGTTCTTCTCA-TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAG-
*
3165335 GCAAAAGGTTGAACAAG
316 GCAAAAGGTTGAACAAA
* *
3165352 CTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
3165409 CTAACTGACA
Statistics
Matches: 336, Mismatches: 31, Indels: 34
0.84 0.08 0.08
Matches are distributed among these distances:
323 8 0.02
324 92 0.27
325 80 0.24
326 7 0.02
327 41 0.12
328 6 0.02
329 10 0.03
330 52 0.15
331 30 0.09
332 1 0.00
333 9 0.03
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.39
Consensus pattern (332 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTAG
AAAAGCTAATCCATCAAGTGATGGATTTCAGCAAAATCTGAACAAATTCTTCTCATTATGAACTT
CTTATCCTTCTTCAGATGAGTTTTCTCATTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTG
ATAGATTAGAGCAAAAGGTTGAACAAATTCTTCTCATTATGACTCTTCTTCCTTCTTCAGATGAG
TTCTTCTCATATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAGGCAAAAGGTT
GAACAAA
Found at i:3166337 original size:75 final size:78
Alignment explanation
Indices: 3166201--3166356 Score: 291
Period size: 75 Copynumber: 2.0 Consensus size: 78
3166191 TATTTCTACT
3166201 ATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAAG-
1 ATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAAGA
3166265 A-ACTTCCAGAAG
66 ACACTTCCAGAAG
3166277 ATGAGCAAATTCATCTTCCAAATTCAATGA-TGGTTTTGCCAAACCAGATCAGATAACTCAAAGA
1 ATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAAGA
3166341 ACACTTCCAGAAG
66 ACACTTCCAGAAG
3166354 ATG
1 ATG
3166357 CTATGAGTCT
Statistics
Matches: 78, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
75 33 0.42
76 31 0.40
77 14 0.18
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (78 bp):
ATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAG
Found at i:3166436 original size:178 final size:180
Alignment explanation
Indices: 3166137--3166459 Score: 605
Period size: 178 Copynumber: 1.8 Consensus size: 180
3166127 GTAGTTCCTA
3166137 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGTCTCTTATTTCTACTA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGTCTCTTATTTCTACTA
*
3166202 TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAAG-A
66 TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAA
3166266 -ACTTCCAGAAGATGAGCAAATTCATCTTCCAAATTCAATGATGGTTTTG
131 CACTTCCAGAAGATGAGCAAATTCATCTTCCAAATTCAATGATGGTTTTG
*
3166315 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGTCTCTTATTTTTACTA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGTCTCTTATTTCTACTA
3166380 TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAA
66 TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAA
*
3166445 CACTTCTAGAAGATG
131 CACTTCCAGAAGATG
3166460 CTATTAGCAC
Statistics
Matches: 140, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
178 126 0.90
179 1 0.01
180 13 0.09
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.28
Consensus pattern (180 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGTCTCTTATTTCTACTA
TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAA
CACTTCCAGAAGATGAGCAAATTCATCTTCCAAATTCAATGATGGTTTTG
Found at i:3166446 original size:103 final size:102
Alignment explanation
Indices: 3166277--3166463 Score: 347
Period size: 103 Copynumber: 1.8 Consensus size: 102
3166267 CTTCCAGAAG
*
3166277 ATGAGCAAATTCATCTTCCAAATTCAATGATGGTTTTGCCAAACCAGATCAGATAACTCAAAGAA
1 ATGAGCAAATTCATCTTCCAAATTCAATGATGGTTCTGCCAAACCAGATCAGATAACTCAAAGAA
3166342 CACTTCCAGAAGATGCTATGAGTCTCTTATTTTTACT
66 CACTTCCAGAAGATGCTATGAGTCTCTTATTTTTACT
3166379 ATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGA
1 ATGAGCAAATTCATCTTCCAAATTCAATGA-TGGTTCTGCCAAACCAGATCAGATAACTCAAAGA
*
3166444 ACACTTCTAGAAGATGCTAT
65 ACACTTCCAGAAGATGCTAT
3166464 TAGCACATTG
Statistics
Matches: 82, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
102 30 0.37
103 52 0.63
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (102 bp):
ATGAGCAAATTCATCTTCCAAATTCAATGATGGTTCTGCCAAACCAGATCAGATAACTCAAAGAA
CACTTCCAGAAGATGCTATGAGTCTCTTATTTTTACT
Found at i:3167624 original size:7 final size:7
Alignment explanation
Indices: 3167612--3167692 Score: 82
Period size: 7 Copynumber: 12.1 Consensus size: 7
3167602 TGACCCCCCC
3167612 TTTTTCT
1 TTTTTCT
3167619 TTTTTCTT
1 TTTTTC-T
3167627 TTTTTCT
1 TTTTTCT
3167634 TTTTTCT
1 TTTTTCT
*
3167641 CTTTT-T
1 TTTTTCT
*
3167647 TTTCTC-
1 TTTTTCT
3167653 TTTTTC-
1 TTTTTCT
3167659 TTTTTCT
1 TTTTTCT
*
3167666 ATTTTC-
1 TTTTTCT
*
3167672 TTTCT-T
1 TTTTTCT
3167678 TTTTTCT
1 TTTTTCT
3167685 TTTTTCT
1 TTTTTCT
3167692 T
1 T
3167693 CAAGCATAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
6 22 0.36
7 32 0.52
8 7 0.11
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTTCT
Found at i:3167629 original size:8 final size:8
Alignment explanation
Indices: 3167612--3167689 Score: 95
Period size: 8 Copynumber: 9.5 Consensus size: 8
3167602 TGACCCCCCC
3167612 TTTTTC-T
1 TTTTTCTT
3167619 TTTTTCTT
1 TTTTTCTT
3167627 TTTTTCTT
1 TTTTTCTT
3167635 TTTTCTCTTT
1 TTTT-TC-TT
*
3167645 TTTTTCTC
1 TTTTTCTT
3167653 TTTTTCTT
1 TTTTTCTT
* *
3167661 TTTCTATT
1 TTTTTCTT
3167669 TTCTTTCTT
1 TT-TTTCTT
3167678 TTTTTCTT
1 TTTTTCTT
3167686 TTTT
1 TTTT
3167690 CTTCAAGCAT
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
7 6 0.10
8 39 0.64
9 10 0.16
10 6 0.10
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTCTT
Found at i:3167663 original size:32 final size:32
Alignment explanation
Indices: 3167612--3167692 Score: 110
Period size: 32 Copynumber: 2.5 Consensus size: 32
3167602 TGACCCCCCC
*
3167612 TTTTTCTTTTTTCTTTTTTTCTTTTTTCTCT-TT
1 TTTTTCTTTTTTC--TTTTTCTATTTTCTCTCTT
*
3167645 TTTTTCTCTTTTTCTTTTTCTATTTTCTTTCTT
1 TTTTTCT-TTTTTCTTTTTCTATTTTCTCTCTT
3167678 TTTTTCTTTTTTCTT
1 TTTTTCTTTTTTCTT
3167693 CAAGCATAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
32 22 0.50
33 16 0.36
34 6 0.14
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.83
Consensus pattern (32 bp):
TTTTTCTTTTTTCTTTTTCTATTTTCTCTCTT
Found at i:3178399 original size:18 final size:20
Alignment explanation
Indices: 3178352--3178399 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
3178342 TGAAATATTA
3178352 ATAAGAAAATATATAAATACT
1 ATAA-AAAATATATAAATACT
* *
3178373 ATGAAAAATA-ATAAGTA-T
1 ATAAAAAATATATAAATACT
3178391 ATAAAAAAT
1 ATAAAAAAT
3178400 TTGAAAAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 9 0.38
19 6 0.25
20 6 0.25
21 3 0.12
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (20 bp):
ATAAAAAATATATAAATACT
Found at i:3179092 original size:13 final size:13
Alignment explanation
Indices: 3179055--3179094 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
3179045 TTGATTTTGA
3179055 AAAATAAATA-TT
1 AAAATAAATATTT
*
3179067 AAAATAATTTATTT
1 AAAATAA-ATATTT
3179081 AAAATAAATATTT
1 AAAATAAATATTT
3179094 A
1 A
3179095 TTTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:3180306 original size:16 final size:16
Alignment explanation
Indices: 3180285--3180316 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3180275 CTGGACCGTT
3180285 GGCTGAGGCGGCTGGA
1 GGCTGAGGCGGCTGGA
*
3180301 GGCTGAGGCGGTTGGA
1 GGCTGAGGCGGCTGGA
3180317 CATGGTGCTA
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:0.12, C:0.16, G:0.56, T:0.16
Consensus pattern (16 bp):
GGCTGAGGCGGCTGGA
Found at i:3180427 original size:9 final size:9
Alignment explanation
Indices: 3180413--3180490 Score: 50
Period size: 9 Copynumber: 8.2 Consensus size: 9
3180403 TTTTTATTAT
3180413 TATTTATAA
1 TATTTATAA
*
3180422 TATTTA-ATG
1 TATTTATA-A
3180431 TATTTAATAA
1 TATTT-ATAA
*
3180441 TAATAATAATAA
1 T-AT--TTATAA
3180453 TATTTATAA
1 TATTTATAA
*
3180462 TAATTATAA
1 TATTTATAA
* *
3180471 TAATAATAA
1 TATTTATAA
*
3180480 TAATTATAA
1 TATTTATAA
3180489 TA
1 TA
3180491 ATAATAGTAA
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
8 1 0.02
9 42 0.75
10 2 0.04
11 5 0.09
12 5 0.09
13 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (9 bp):
TATTTATAA
Found at i:3180443 original size:3 final size:3
Alignment explanation
Indices: 3180435--3180503 Score: 93
Period size: 3 Copynumber: 23.0 Consensus size: 3
3180425 TTAATGTATT
* * *
3180435 TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
3180483 TTA TAA TAA TAA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
3180504 ATCAAAATGG
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:3182502 original size:2 final size:2
Alignment explanation
Indices: 3182495--3182552 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
3182485 TCAATGTCAA
3182495 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
3182537 AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT A
3182553 ATTCATACTA
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3185647 original size:14 final size:15
Alignment explanation
Indices: 3185615--3185647 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3185605 TTATTTTTCT
3185615 TAAAAGTAATTTATA
1 TAAAAGTAATTTATA
*
3185630 TAAAATTAATTT-TA
1 TAAAAGTAATTTATA
3185644 TAAA
1 TAAA
3185648 TAGGATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
TAAAAGTAATTTATA
Found at i:3185811 original size:15 final size:16
Alignment explanation
Indices: 3185766--3185818 Score: 56
Period size: 14 Copynumber: 3.4 Consensus size: 16
3185756 AATAATAATA
3185766 ATTAAAATGAAAGAA-
1 ATTAAAATGAAAGAAT
* *
3185781 ATT-AAAGGAAATAAT
1 ATTAAAATGAAAGAAT
*
3185796 ATTAAAATGAAAAATAT
1 ATTAAAATGAAAGA-AT
3185813 ATTAAA
1 ATTAAA
3185819 TAAAAAAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 9 0.29
15 6 0.19
16 8 0.26
17 8 0.26
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.26
Consensus pattern (16 bp):
ATTAAAATGAAAGAAT
Found at i:3185825 original size:16 final size:18
Alignment explanation
Indices: 3185789--3185825 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
3185779 AAATTAAAGG
*
3185789 AAATAATATTAAAATGAA
1 AAATAATATTAAAATAAA
3185807 AAAT-ATATT-AAATAAA
1 AAATAATATTAAAATAAA
3185823 AAA
1 AAA
3185826 ACAAACTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 9 0.50
17 5 0.28
18 4 0.22
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (18 bp):
AAATAATATTAAAATAAA
Found at i:3187080 original size:3 final size:3
Alignment explanation
Indices: 3187074--3187112 Score: 51
Period size: 3 Copynumber: 12.0 Consensus size: 3
3187064 TTTATTTTTT
3187074 TAA TAA TAA TAA TATA TATA TAA TACA TAA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TA-A TAA TA-A TAA TAA TAA TAA
3187113 AATGAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 24 0.71
4 10 0.29
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3187574 original size:37 final size:36
Alignment explanation
Indices: 3187505--3187858 Score: 284
Period size: 37 Copynumber: 9.7 Consensus size: 36
3187495 AAAATAAGTC
* * *
3187505 GAAATAACTGTCTCAAGTGAGACAAATCTTTGTTTTAT
1 GAAA-AACAGTCTCAAGTGAGATAAAT-TTTGTTTTAA
*
3187543 GAAAAACAGTCTCAAGTGAGATAAATTTTTGTTTCAA
1 GAAAAACAGTCTCAAGTGAGATAAA-TTTTGTTTTAA
** * * * *
3187580 GTGAAACTGTCTCAAGCGAGACAAAATTTGTTTTAA
1 GAAAAACAGTCTCAAGTGAGATAAATTTTGTTTTAA
* * *
3187616 GAAAAACAATCTCAAGTGAGATAAAGTTCTG-TTT-C
1 GAAAAACAGTCTCAAGTGAGATAAA-TTTTGTTTTAA
* * *
3187651 GAATGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAA
1 GAA--AAACAGTCTCAAGTGAGATAAATTTTGTTTTAA
* * **
3187689 GAAAAACAATCTCAAGTGAGATAAAGTTCTGTTTCGA
1 GAAAAACAGTCTCAAGTGAGATAAA-TTTTGTTTTAA
** * * *
3187726 GTGAAACTGTCTCAAGCGAGAGAAATTTTGTTTTAA
1 GAAAAACAGTCTCAAGTGAGATAAATTTTGTTTTAA
* * * **
3187762 CAAAAACAATCTCAAGTGAGATAAAGTTCTGTTTCGA
1 GAAAAACAGTCTCAAGTGAGATAAA-TTTTGTTTTAA
** * * *
3187799 GTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAA
1 GAAAAACAGTCTCAAGTGAGATAAATTTTGTTTTAA
3187835 GAAAAGA-A-TCTCAAGTGAGATAAA
1 GAAAA-ACAGTCTCAAGTGAGATAAA
3187859 GTTCTGTGAA
Statistics
Matches: 240, Mismatches: 67, Indels: 21
0.73 0.20 0.06
Matches are distributed among these distances:
35 17 0.07
36 90 0.38
37 125 0.52
38 8 0.03
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.30
Consensus pattern (36 bp):
GAAAAACAGTCTCAAGTGAGATAAATTTTGTTTTAA
Found at i:3187630 original size:73 final size:73
Alignment explanation
Indices: 3187510--3187865 Score: 581
Period size: 73 Copynumber: 4.9 Consensus size: 73
3187500 AAGTCGAAAT
* * * * *
3187510 AACTGTCTCAAGTGAGACAAATCTTTGTTTTATGAAAAACAGTCTCAAGTGAGATAAATTTTTGT
1 AACTGTCTCAAGCGAGACAAAT-TTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGT
3187575 TTCAAGTGA
65 TTCAAGTGA
*
3187584 AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
1 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
3187649 TCGAA-TGA
66 TC-AAGTGA
3187657 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
1 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
*
3187722 TCGAGTGA
66 TCAAGTGA
* *
3187730 AACTGTCTCAAGCGAGAGAAATTTTGTTTTAACAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
1 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
*
3187795 TCGAGTGA
66 TCAAGTGA
*
3187803 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAG-AAAAGAATCTCAAGTGAGATAAAGTTCTGT
1 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGT
3187866 GAAAACATCC
Statistics
Matches: 267, Mismatches: 13, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
72 30 0.11
73 215 0.81
74 22 0.08
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (73 bp):
AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
TCAAGTGA
Found at i:3188150 original size:165 final size:165
Alignment explanation
Indices: 3187900--3188224 Score: 508
Period size: 165 Copynumber: 2.0 Consensus size: 165
3187890 TATGGATGTG
* * * *
3187900 GGAAATAGTTTACTAAGTAAGATACTATGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTC
1 GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTC
** *
3187965 AGAAAAGATTGAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAATAACATGTTGAT
66 AGAAAAGATAAAATGAGAAACTATGAAAATCATTTTCTCATTATTTTTCAAAATAACATGTTGAT
* *
3188030 TGGGTAACATGCCCCAATCTCAAGATAATGTTGTT
131 TGGGTAACATGACCAAATCTCAAGATAATGTTGTT
*
3188065 GGAAATAGTTTACTAAGTAAAAAAACTAAGAAAATTGTTTTCTTACTTTTCAACAATTTCATTTT
1 GGAAATAGTTTACTAAGT-AAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTT
* * * *
3188130 C-GAAAATATAAAATGAGAAACTATGGAAATCATTTTCTCATTATTTTTCAGAATATCATGTTGA
65 CAGAAAAGATAAAATGAGAAACTATGAAAATCATTTTCTCATTATTTTTCAAAATAACATGTTGA
3188194 TTGGGTAACATGACCAAATCTCAAGATAATG
130 TTGGGTAACATGACCAAATCTCAAGATAATG
3188225 CTCATTCTTG
Statistics
Matches: 145, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
165 103 0.71
166 42 0.29
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.36
Consensus pattern (165 bp):
GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTC
AGAAAAGATAAAATGAGAAACTATGAAAATCATTTTCTCATTATTTTTCAAAATAACATGTTGAT
TGGGTAACATGACCAAATCTCAAGATAATGTTGTT
Found at i:3188761 original size:22 final size:22
Alignment explanation
Indices: 3188736--3188790 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
3188726 AATAAAGTTT
3188736 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
3188758 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
3188780 TCATCTTTGAA
1 TCATCTTTGAA
3188791 GAGTGTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:3192181 original size:18 final size:18
Alignment explanation
Indices: 3192158--3192193 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3192148 AGGAATGATA
3192158 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
3192176 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
3192194 ATATGTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:3192216 original size:121 final size:121
Alignment explanation
Indices: 3192055--3192539 Score: 880
Period size: 121 Copynumber: 4.0 Consensus size: 121
3192045 CGAGGGTCTA
3192055 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
3192120 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
* *
3192176 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACGCATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
3192241 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
3192297 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
* * * * *
3192362 GATCCTTGGCATATGTATATGATTCTTAAGGAATGATATGTAGTTCTTCGGGACAT
66 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
*
3192418 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
**
3192483 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACAT
66 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
3192539 T
1 T
3192540 ATTATATGGC
Statistics
Matches: 347, Mismatches: 17, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
121 347 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (121 bp):
TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
Found at i:3192302 original size:18 final size:18
Alignment explanation
Indices: 3192279--3192314 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3192269 AGGAATGATA
3192279 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
3192297 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
3192315 ATATGTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:3192616 original size:23 final size:23
Alignment explanation
Indices: 3192547--3192604 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
3192537 ATTATTATAT
*
3192547 GGCACTACGGTGCAATTCTATGC
1 GGCACTACGGTGCAATTCTATGA
3192570 GGCACTACGGTGCAATTCTATGA
1 GGCACTACGGTGCAATTCTATGA
*
3192593 GGCACTTCGGTG
1 GGCACTACGGTG
3192605 TATTTATATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.21, C:0.24, G:0.29, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTATGA
Found at i:3196593 original size:26 final size:25
Alignment explanation
Indices: 3196562--3196611 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
3196552 CTCCCATTTT
3196562 TCTTTTTCCTTTTTTTTCCTTTTTCA
1 TCTTTTTCC-TTTTTTTCCTTTTTCA
* *
3196588 TCTTTTTTCTTTTTTTCTTTTTTC
1 TCTTTTTCCTTTTTTTCCTTTTTC
3196612 TTTCTTTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (25 bp):
TCTTTTTCCTTTTTTTCCTTTTTCA
Found at i:3196617 original size:26 final size:26
Alignment explanation
Indices: 3196560--3196644 Score: 82
Period size: 26 Copynumber: 3.3 Consensus size: 26
3196550 TTCTCCCATT
* *
3196560 TTTCTTTTTCCTTTTTTTTCCTTTTTC
1 TTTCTTTTTTC-TTTTTTTCTTTTTTC
*
3196587 -ATCTTTTTTCTTTTTTTCTTTTTTC
1 TTTCTTTTTTCTTTTTTTCTTTTTTC
** ***
3196612 TTTCTTTACTGGATTTTTCTTTTTTC
1 TTTCTTTTTTCTTTTTTTCTTTTTTC
3196638 TTTCTTT
1 TTTCTTT
3196645 GCTGGATTTT
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
25 14 0.29
26 34 0.71
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.76
Consensus pattern (26 bp):
TTTCTTTTTTCTTTTTTTCTTTTTTC
Found at i:3196637 original size:7 final size:7
Alignment explanation
Indices: 3196558--3196640 Score: 58
Period size: 7 Copynumber: 10.3 Consensus size: 7
3196548 ATTTCTCCCA
3196558 TTTTTCT
1 TTTTTCT
*
3196565 TTTTCCTTT
1 TTTT--TCT
3196574 TTTTTCCT
1 TTTTT-CT
3196582 TTTTCATCT
1 TTTT--TCT
3196591 TTTTTCTT
1 TTTTTC-T
3196599 TTTTTCT
1 TTTTTCT
3196606 TTTTTCT
1 TTTTTCT
3196613 TTCTTTACT
1 TT-TTT-CT
3196622 GGATTTTTCT
1 ---TTTTTCT
3196632 TTTTTCT
1 TTTTTCT
3196639 TT
1 TT
3196641 CTTTGCTGGA
Statistics
Matches: 63, Mismatches: 2, Indels: 22
0.72 0.02 0.25
Matches are distributed among these distances:
7 26 0.41
8 15 0.24
9 14 0.22
10 3 0.05
11 3 0.05
12 2 0.03
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.77
Consensus pattern (7 bp):
TTTTTCT
Found at i:3196649 original size:26 final size:26
Alignment explanation
Indices: 3196599--3196677 Score: 140
Period size: 26 Copynumber: 3.0 Consensus size: 26
3196589 CTTTTTTCTT
*
3196599 TTTTTCTTTTTTCTTTCTTTACTGGA
1 TTTTTCTTTTTTCTTTCTTTGCTGGA
3196625 TTTTTCTTTTTTCTTTCTTTGCTGGA
1 TTTTTCTTTTTTCTTTCTTTGCTGGA
*
3196651 TTTTTCTTTCTTCTTTCTTTGCTGGA
1 TTTTTCTTTTTTCTTTCTTTGCTGGA
3196677 T
1 T
3196678 GAGTATAAGA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 51 1.00
ACGTcount: A:0.05, C:0.16, G:0.10, T:0.68
Consensus pattern (26 bp):
TTTTTCTTTTTTCTTTCTTTGCTGGA
Found at i:3202361 original size:14 final size:15
Alignment explanation
Indices: 3202329--3202361 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3202319 TTATTTTTCT
3202329 TAAAAGTAATTTATA
1 TAAAAGTAATTTATA
*
3202344 TAAAATTAATTT-TA
1 TAAAAGTAATTTATA
3202358 TAAA
1 TAAA
3202362 TAGGATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
TAAAAGTAATTTATA
Found at i:3203819 original size:3 final size:3
Alignment explanation
Indices: 3203813--3203877 Score: 69
Period size: 3 Copynumber: 21.0 Consensus size: 3
3203803 TTTATTTTTT
*
3203813 TAA TAA TAA TAA TAA T-A TATA TATA TAA TACA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TA-A TAA TA-A TAA TAA TAA TAA TAA
**
3203860 TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
3203878 AATGAAAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.04
3 41 0.77
4 10 0.19
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:3209101 original size:13 final size:13
Alignment explanation
Indices: 3209083--3209109 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3209073 TTACAGACGC
3209083 GCATATGAAGACT
1 GCATATGAAGACT
3209096 GCATATGAAGACT
1 GCATATGAAGACT
3209109 G
1 G
3209110 TTCAACTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:3210601 original size:38 final size:38
Alignment explanation
Indices: 3210547--3210627 Score: 108
Period size: 38 Copynumber: 2.1 Consensus size: 38
3210537 GCTACAGTAC
* * *
3210547 ACCCCAAAGATACATTGCAGTCCATGTGTCTCTCCCCT
1 ACCCCAAAGATACATTGAACTCCATGCGTCTCTCCCCT
* * *
3210585 ACCCCGAAGATGCATTGAACTCCATGCGTCTCTCCTCT
1 ACCCCAAAGATACATTGAACTCCATGCGTCTCTCCCCT
3210623 ACCCC
1 ACCCC
3210628 CCGAAGACAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.22, C:0.40, G:0.14, T:0.25
Consensus pattern (38 bp):
ACCCCAAAGATACATTGAACTCCATGCGTCTCTCCCCT
Found at i:3210898 original size:18 final size:18
Alignment explanation
Indices: 3210877--3210931 Score: 53
Period size: 18 Copynumber: 3.0 Consensus size: 18
3210867 GGGGCACCAG
3210877 GGAGAAGAAAGAAA-AATA
1 GGAGAAGAAAGAAAGAA-A
3210895 GGAGAATG-AAGAAAGAAA
1 GGAGAA-GAAAGAAAGAAA
3210913 GGAAGAAG-AAGAAGAGAAA
1 GG-AGAAGAAAGAA-AGAAA
3210932 AGAAGAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
18 21 0.64
19 12 0.36
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.04
Consensus pattern (18 bp):
GGAGAAGAAAGAAAGAAA
Found at i:3210922 original size:22 final size:21
Alignment explanation
Indices: 3210879--3210927 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
3210869 GGCACCAGGG
*
3210879 AGAAGAAAGAAAAATAGGAGA
1 AGAAGAAAGAAAAATAGAAGA
*
3210900 ATGAAGAAAGAAAGGA-AGAAGA
1 A-GAAGAAAGAAA-AATAGAAGA
3210922 AGAAGA
1 AGAAGA
3210928 GAAAAGAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 6 0.25
22 17 0.71
23 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.31, T:0.04
Consensus pattern (21 bp):
AGAAGAAAGAAAAATAGAAGA
Found at i:3210946 original size:12 final size:13
Alignment explanation
Indices: 3210918--3210951 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
3210908 AGAAAGGAAG
3210918 AAGAAGAAGAGAA
1 AAGAAGAAGAGAA
*
3210931 AAGAAGAATA-AA
1 AAGAAGAAGAGAA
3210943 AAGAAGAAG
1 AAGAAGAAG
3210952 GGAAGAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.03
Consensus pattern (13 bp):
AAGAAGAAGAGAA
Found at i:3211204 original size:18 final size:19
Alignment explanation
Indices: 3211169--3211213 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
3211159 GTTATGGTGT
*
3211169 TATTATTATTTAA-TAAAA
1 TATTATTATTTAAGAAAAA
* *
3211187 TATTCTTATTTGAGAAAAA
1 TATTATTATTTAAGAAAAA
3211206 TATTATTA
1 TATTATTA
3211214 GTAAATGGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (19 bp):
TATTATTATTTAAGAAAAA
Found at i:3214325 original size:20 final size:20
Alignment explanation
Indices: 3214300--3214338 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
3214290 AACTAATAAA
3214300 CCATAAATC-ATAGACAATAG
1 CCATAAA-CAATAGACAATAG
3214320 CCATAAACAATAGACAATA
1 CCATAAACAATAGACAATA
3214339 ATCCAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.54, C:0.21, G:0.08, T:0.18
Consensus pattern (20 bp):
CCATAAACAATAGACAATAG
Found at i:3214524 original size:59 final size:59
Alignment explanation
Indices: 3214399--3214527 Score: 143
Period size: 59 Copynumber: 2.2 Consensus size: 59
3214389 CATAATGCAA
* * **
3214399 TCCCGAGTATGACACATAAGGTCGTGTCCACCATCTGTACTAGATATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCGTGTCCACCATATACACTAGATATCCTTAAGTACAG
* * * * ** *
3214458 TCTCGAATATGACACATAAGGTTGT-TCCCACCATATACACTAGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCGTGT-CCACCATATACACTAGATATCCTTAAGTACAG
3214517 TCCCGAATATG
1 TCCCGAATATG
3214528 CAACCTGCTG
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
58 1 0.02
59 56 0.98
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCGTGTCCACCATATACACTAGATATCCTTAAGTACAG
Found at i:3217174 original size:6 final size:6
Alignment explanation
Indices: 3217163--3217228 Score: 55
Period size: 6 Copynumber: 10.7 Consensus size: 6
3217153 ATCTCTAGAT
* * *
3217163 TTTTTC TTTTTC TATTTC CTTTTC -TTTTC TTTTTC TGCTTTTT TCTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC T--TTTTC T-TTTTC
3217213 TTTTTC TCTTTT- TTTT
1 TTTTTC T-TTTTC TTTT
3217229 ATTACATATT
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
5 8 0.16
6 28 0.55
7 10 0.20
8 5 0.10
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.79
Consensus pattern (6 bp):
TTTTTC
Found at i:3217227 original size:21 final size:21
Alignment explanation
Indices: 3217164--3217227 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 21
3217154 TCTCTAGATT
*
3217164 TTTTCTTTTTCTATTTCCTTTTC
1 TTTTCTTTTTCTCTTT--TTTTC
3217187 TTTTCTTTTTCTGC-TTTTTTC
1 TTTTCTTTTTCT-CTTTTTTTC
3217208 TTTTCTTTTTCTCTTTTTTT
1 TTTTCTTTTTCTCTTTTTTT
3217228 TATTACATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
20 1 0.03
21 23 0.61
23 14 0.37
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.78
Consensus pattern (21 bp):
TTTTCTTTTTCTCTTTTTTTC
Found at i:3219994 original size:20 final size:20
Alignment explanation
Indices: 3219969--3220010 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
3219959 AACTAATAAA
*
3219969 CCATAAACCATAGACAATAG
1 CCATAAACAATAGACAATAG
*
3219989 CCATAAATAATAGACAATAG
1 CCATAAACAATAGACAATAG
3220009 CC
1 CC
3220011 CAATATACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.24, G:0.10, T:0.17
Consensus pattern (20 bp):
CCATAAACAATAGACAATAG
Found at i:3223674 original size:24 final size:24
Alignment explanation
Indices: 3223647--3223722 Score: 66
Period size: 24 Copynumber: 3.0 Consensus size: 24
3223637 ACTTTAACTT
*
3223647 TCTTCTCTTATTCTTCTTTCTTTC
1 TCTTCTCTTCTTCTTCTTTCTTTC
*
3223671 TCTTTTCTCTTCTTCCTTCCTTCATTT-
1 TC--TTCTCTTCTT-CTTCTTTC-TTTC
*
3223698 T-TTTTCTTCTTCTTCATTTCTTTC
1 TCTTCTCTTCTTCTTC-TTTCTTTC
3223722 T
1 T
3223723 TCTCACCGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
23 7 0.17
24 15 0.36
26 9 0.21
27 8 0.19
28 3 0.07
ACGTcount: A:0.04, C:0.29, G:0.00, T:0.67
Consensus pattern (24 bp):
TCTTCTCTTCTTCTTCTTTCTTTC
Found at i:3224324 original size:17 final size:17
Alignment explanation
Indices: 3224304--3224349 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
3224294 TATTAATGGA
3224304 GTAAAAAAATAAAAAAG
1 GTAAAAAAATAAAAAAG
* *
3224321 GTAAAGAAATTAAAAAG
1 GTAAAAAAATAAAAAAG
3224338 G-AATAAAAATAA
1 GTAA-AAAAATAA
3224350 TGTGTACATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
16 2 0.08
17 22 0.92
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (17 bp):
GTAAAAAAATAAAAAAG
Found at i:3224621 original size:8 final size:8
Alignment explanation
Indices: 3224608--3224642 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
3224598 AGAAAAATTA
*
3224608 ATACATCT
1 ATACATAT
3224616 ATACATAT
1 ATACATAT
3224624 ATACATAT
1 ATACATAT
*
3224632 ATATATAT
1 ATACATAT
3224640 ATA
1 ATA
3224643 TAATTATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (8 bp):
ATACATAT
Found at i:3224633 original size:2 final size:2
Alignment explanation
Indices: 3224615--3224687 Score: 61
Period size: 2 Copynumber: 40.0 Consensus size: 2
3224605 TTAATACATC
* *
3224615 TA TA CA TA TA TA CA TA TA TA TA TA TA TA TA -A T- TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
3224654 GA TA TA TA TA -A TA TA -A TA TA AA TA -A TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3224688 AATAAAAAAG
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
1 7 0.12
2 50 0.88
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (2 bp):
TA
Found at i:3224650 original size:16 final size:15
Alignment explanation
Indices: 3224615--3224687 Score: 68
Period size: 14 Copynumber: 5.1 Consensus size: 15
3224605 TTAATACATC
*
3224615 TATACATATATACATA
1 TATATATATATA-ATA
3224631 TATATATATAT-ATA
1 TATATATATATAATA
3224645 -AT-TATATA-AGATA
1 TATATATATATA-ATA
3224658 TATATA-ATATAATA
1 TATATATATATAATA
*
3224672 TAAATA-ATATAATA
1 TATATATATATAATA
3224686 TA
1 TA
3224688 AATAAAAAAG
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
12 6 0.12
13 5 0.10
14 26 0.52
15 3 0.06
16 10 0.20
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (15 bp):
TATATATATATAATA
Found at i:3224660 original size:19 final size:20
Alignment explanation
Indices: 3224630--3224693 Score: 82
Period size: 19 Copynumber: 3.4 Consensus size: 20
3224620 ATATATACAT
*
3224630 ATATATATATATATAAT-T-
1 ATATAAATATATATAATATA
3224648 ATATAAGATATATATAATATA
1 ATATAA-ATATATATAATATA
3224669 ATATAAATA-ATATAATATA
1 ATATAAATATATATAATATA
3224688 A-ATAAA
1 ATATAAA
3224694 AAAGGAATAT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
18 10 0.24
19 22 0.52
20 4 0.10
21 6 0.14
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
ATATAAATATATATAATATA
Found at i:3224660 original size:21 final size:20
Alignment explanation
Indices: 3224615--3224688 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 20
3224605 TTAATACATC
* *
3224615 TATACATAT-ATACATATATA
1 TATATATATAATA-ATATAAA
*
3224635 TATATATATAATTATATAAGA
1 TATATATATAATAATATAA-A
3224656 TATATATA-ATATAATATAAA
1 TATATATATA-ATAATATAAA
3224676 TAATATAATATAA
1 T-ATAT-ATATAA
3224689 ATAAAAAAGG
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
20 16 0.36
21 23 0.52
22 4 0.09
23 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (20 bp):
TATATATATAATAATATAAA
Found at i:3224722 original size:20 final size:20
Alignment explanation
Indices: 3224686--3224724 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3224676 TAATATAATA
*
3224686 TAAATAAAAAAGGAATATAG
1 TAAATAAAAAAGAAATATAG
3224706 TAAATAAATAAA-AAATATA
1 TAAATAAA-AAAGAAATATA
3224725 ATTAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (20 bp):
TAAATAAAAAAGAAATATAG
Found at i:3226251 original size:110 final size:106
Alignment explanation
Indices: 3226047--3226295 Score: 311
Period size: 110 Copynumber: 2.3 Consensus size: 106
3226037 TATTGTTCCA
* * * * * *
3226047 AGTCCAATATCCTCCGTTGTGAAGTTGGAATTGGCTCTGGAACTGGGAAATTGTTTGTTGATAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGGAACTGGAAAATTGTTTGTTGACAAC
*
3226112 CAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTATTGTCTCG
66 CAGTCGCCCCTTCGCTGTGAAGTTAAGCTTGTATTGTCTCG
* *
3226153 AGTTCAATATCCTTCGTTTTGAAGTTGAAATTGACTCTGAATGAGACT-GAAAAGTTGTTTGTTG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTG---GA-ACTGGAAAA-TTGTTTGTTG
* * * *
3226217 ACAATCAGTCGCCCCTTCGTTGTGAAGTTAAGCTTGTGTTGTCTTG
61 ACAACCAGTCGCCCCTTCGCTGTGAAGTTAAGCTTGTATTGTCTCG
* *
3226263 AGTCCAATATCCCTCGCTGTGAAGTTGAAATTG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
3226296 GCTGTGAAAT
Statistics
Matches: 121, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
106 34 0.28
109 6 0.05
110 81 0.67
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.35
Consensus pattern (106 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGGAACTGGAAAATTGTTTGTTGACAAC
CAGTCGCCCCTTCGCTGTGAAGTTAAGCTTGTATTGTCTCG
Found at i:3227185 original size:63 final size:66
Alignment explanation
Indices: 3227045--3227334 Score: 196
Period size: 65 Copynumber: 4.3 Consensus size: 66
3227035 CTCAAAGGAA
** *
3227045 ACAAAATTTGTTTTAAGGGAAATAAATTTGAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGG
1 ACAAAATTTGTTTTAAGGGAAATAAATTCAAAGA-TTTGTGTTTCAAGAGAAACTGTCTCAAGAG
3227110 AG
65 AG
* * *
3227112 ACAAAATTTGTTTTAGGGGAAATAAATTCAAAGA-TT-T-TTTCAAGGGAAACTGTCTCGAGAGA
1 ACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTGTGTTTCAAGAGAAACTGTCTCAAGAGA
3227174 G
66 G
** * * ** * * *
3227175 ACGGAATTTGTTTCAAGAGAAACTGTCCCAAGAGAGACAAA-ACTT-AGTTCCAAGAGAAACTGT
1 ACAAAATTTGTTTTAAGGGAAA---T----A-A-ATTCAAAGATTTGTGTTTCAAGAGAAACTGT
*
3227238 CTCAAGGGAG
57 CTCAAGAGAG
** * *** * * * * *
3227248 ATGAAATTTGTTTCAAATAAAACATATTCAAATAATT-TGTTTCAAGGGAAACTGTCTCAAGAGA
1 ACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTGTGTTTCAAGAGAAACTGTCTCAAGAGA
3227312 G
66 G
*
3227313 ACAAAATTTGTTTCAAGGGAAA
1 ACAAAATTTGTTTTAAGGGAAA
3227335 CTATCTCAAG
Statistics
Matches: 174, Mismatches: 37, Indels: 26
0.73 0.16 0.11
Matches are distributed among these distances:
63 40 0.23
64 6 0.03
65 46 0.26
66 2 0.01
67 31 0.18
70 1 0.01
71 2 0.01
72 7 0.04
73 39 0.22
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (66 bp):
ACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTGTGTTTCAAGAGAAACTGTCTCAAGAGA
G
Found at i:3227197 original size:36 final size:36
Alignment explanation
Indices: 3227145--3227472 Score: 201
Period size: 36 Copynumber: 9.5 Consensus size: 36
3227135 AAATTCAAAG
* * *
3227145 ATTT-TTTCAAGGGAAACTGTCTCGAGAGAGACGGA
1 ATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAA
* *
3227180 ATTTGTTTCAAGAGAAACTGTCCCAAGAGAGACAAA
1 ATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAA
* * * *
3227216 ACTTAGTTCCAAGAGAAACTGTCTCAAGGGAGATGAA
1 A-TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAA
* * *
3227253 ATTTGTTTCAA-ATAAAACATAT-TC---A-A-A--TA
1 ATTTGTTTCAAGA-GAAAC-TGTCTCAAGAGAGACGAA
* *
3227282 ATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA
1 ATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAA
* * *
3227318 ATTTGTTTCAAGGGAAACTATCTCAAGAGAGATGAA
1 ATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAA
* * *
3227354 ATTTATTTCAAG-GCAAA-TGTTTTC-----A-ATG--
1 ATTTGTTTCAAGAG-AAACTG-TCTCAAGAGAGACGAA
* * *
3227382 TTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAA
1 ATT-TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAA
* * * *
3227419 ATTTTGTTTTAAGGGAAACTATCTCAAGAGAGACAAA
1 A-TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAA
*
3227456 ATTTGTTTCAAGGGAAA
1 ATTTGTTTCAAGAGAAA
3227473 TGTTTTCAAT
Statistics
Matches: 228, Mismatches: 38, Indels: 53
0.71 0.12 0.17
Matches are distributed among these distances:
28 4 0.02
29 32 0.14
30 6 0.03
31 2 0.01
32 2 0.01
33 1 0.00
34 2 0.01
35 8 0.04
36 107 0.47
37 62 0.27
38 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (36 bp):
ATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAA
Found at i:3227237 original size:37 final size:36
Alignment explanation
Indices: 3227152--3227248 Score: 113
Period size: 37 Copynumber: 2.7 Consensus size: 36
3227142 AAGATTTTTT
* * ** * *
3227152 CAAGGGAAACTGTCTCGAGAGAGACGGAATTTGTTT
1 CAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
*
3227188 CAAGAGAAACTGTCCCAAGAGAGACAAAACTTAGTTC
1 CAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGTTC
*
3227225 CAAGAGAAACTGTCTCAAGGGAGA
1 CAAGAGAAACTGTCTCAAGAGAGA
3227249 TGAAATTTGT
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
36 24 0.47
37 27 0.53
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.19
Consensus pattern (36 bp):
CAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
Found at i:3227258 original size:136 final size:138
Alignment explanation
Indices: 3227089--3227349 Score: 364
Period size: 138 Copynumber: 1.9 Consensus size: 138
3227079 TTTTGTGTTT
* ** * * *
3227089 CAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAA-GATTT-TTT
1 CAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAATAATTTGTTT
* ** *
3227152 CAAGGGAAACTGTCTCGAGAGAGACGGAATTTGTTTCAAGAGAAACTGTCCCAAGAGAGACAAAA
66 CAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTATCCCAAGAGAGACAAAA
3227217 CTTAGTTC
131 CTTAGTTC
** * *
3227225 CAAGAGAAACTGTCTCAAGGGAGATGAAATTTGTTTCAAATAAAACATATTCAAATAATTTGTTT
1 CAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAATAATTTGTTT
* *
3227290 CAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGA
66 CAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTATCCCAAGAGAGA
3227350 TGAAATTTAT
Statistics
Matches: 107, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
136 46 0.43
137 4 0.04
138 57 0.53
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (138 bp):
CAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAATAATTTGTTT
CAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTATCCCAAGAGAGACAAAA
CTTAGTTC
Found at i:3227437 original size:37 final size:37
Alignment explanation
Indices: 3227386--3227661 Score: 173
Period size: 37 Copynumber: 7.9 Consensus size: 37
3227376 TCAATGTTTA
* *
3227386 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* *
3227423 TGTTTTAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* *
3227459 TGTTTCAAGGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* * * *
3227487 ATGTTTTAAGAGAAACTGTCTCAAGGGAGATAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
3227525 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * *
3227561 CATTTCAAGGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* * *
3227589 ATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* * *
3227627 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
3227662 CTTCTTTTTA
Statistics
Matches: 180, Mismatches: 33, Indels: 52
0.68 0.12 0.20
Matches are distributed among these distances:
28 4 0.02
29 29 0.16
30 5 0.03
32 2 0.01
33 2 0.01
34 2 0.01
35 4 0.02
36 35 0.19
37 91 0.51
38 6 0.03
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.31
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:3227465 original size:102 final size:102
Alignment explanation
Indices: 3227183--3227661 Score: 656
Period size: 102 Copynumber: 4.7 Consensus size: 102
3227173 AGACGGAATT
* * * * * * * *
3227183 TGTTTCAAGAGAAACTGTCCCAAGAGAGACAAAACTTAGTTCCAAGAGAAACTGTCTCAAGGGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
* * *** ** * **
3227248 ATGAAATTTGTTTCAAATAAAACATATTCAAATAATT-
66 ATAAAATTTATTTCAAGGGAAATGTTTTC-AATGTTTA
* *
3227285 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
* *
3227349 ATGAAATTTATTTCAAGGCAAATGTTTTCAATGTTTA
66 ATAAAATTTATTTCAAGGGAAATGTTTTCAATGTTTA
*
3227386 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTTAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
* *
3227451 ACAAAATTTGTTTCAAGGGAAATGTTTTCAATGTTTA
66 ATAAAATTTATTTCAAGGGAAATGTTTTCAATGTTTA
* *
3227488 TGTTTTAAGAGAAACTGTCTCAAGGGAGATAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
* *
3227553 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
66 ATAAAATTTATTTCAAGGGAAATGTTTTCAATGTTTA
* *
3227590 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGCGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
3227655 ATAAAAT
66 ATAAAAT
3227662 CTTCTTTTTA
Statistics
Matches: 342, Mismatches: 33, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
100 5 0.01
101 79 0.23
102 258 0.75
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.30
Consensus pattern (102 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
ATAAAATTTATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:3229175 original size:61 final size:64
Alignment explanation
Indices: 3229099--3229228 Score: 167
Period size: 69 Copynumber: 2.0 Consensus size: 64
3229089 TGTCTCTCTC
3229099 TTGATGATCTATGATCTT-TG-AGTGG-AGTGATTCAGAAATGATTGTGCTTGATCAATCTCAT
1 TTGATGATCTATGATCTTGTGAAGTGGTAGTGATTCAGAAATGATTGTGCTTGATCAATCTCAT
* * *
3229160 TTGATGCTCTATGATCTTCGAGTGAAGTGGTTCAGTGATTCGGCAATGATTGTGCTTGATCAATC
1 TTGATGATCTATGATCTT---GTGAAGTGG-T-AGTGATTCAGAAATGATTGTGCTTGATCAATC
3229225 TCAT
61 TCAT
3229229 AGTTTGAATC
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
61 17 0.29
65 2 0.03
66 5 0.09
69 34 0.59
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (64 bp):
TTGATGATCTATGATCTTGTGAAGTGGTAGTGATTCAGAAATGATTGTGCTTGATCAATCTCAT
Found at i:3229324 original size:21 final size:21
Alignment explanation
Indices: 3229289--3229346 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
3229279 TCTTGTTTTC
*
3229289 TTTTTTC-TTTAATTTTCCTT
1 TTTTTTCTTTTTATTTTCCTT
*
3229309 TTTTTTCTTTTTATTTTTTCTT
1 TTTTTTCTTTTTA-TTTTCCTT
3229331 TTTTTCTCTTTTTATT
1 TTTTT-TCTTTTTATT
3229347 CTGATTTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.21
21 4 0.12
22 14 0.42
23 8 0.24
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTTTTCTTTTTATTTTCCTT
Found at i:3229326 original size:33 final size:32
Alignment explanation
Indices: 3229284--3229348 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
3229274 ATGCATCTTG
* *
3229284 TTTTCTTTTTTCTTTAATTTTC-CTTTTTTTTCT
1 TTTTATTTTTTCTTT--TTTTCTCTTTTTATTCT
3229317 TTTTATTTTTTCTTTTTTTCTCTTTTTATTCT
1 TTTTATTTTTTCTTTTTTTCTCTTTTTATTCT
3229349 GATTTAATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 5 0.17
32 10 0.34
33 14 0.48
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (32 bp):
TTTTATTTTTTCTTTTTTTCTCTTTTTATTCT
Done.